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E580 User`s Manual

1. Figure 4 18 The polynomial baseline fitting task bar t 6 v ET E v ono secondary gt ler FS feno Resun ILU W fauaiRegions 10 000 10 000 5 000 5 000 T 0 So f gt o 5 000 5 000 i 10 000 10 000 Ss O a A LLL tt sje o 500 1 000 1500 zo0 S R o 500 1 000 1500 2 000 Intensity Viewport 1 Time ns Intensity Viewport 3 Time ns Figure 4 19 Selecting the baseline for fitting 4 16 s i Processing the FID eee Fs ivie ES sno Secondary gt Fit a constant to the baseline Click the Oth Order button in the task bar A fitted horizontal line appears Subtract the baseline Click the Subtract Line button in the task bar The subtraction result appears in the result dataset Transfer the result to primary Click the Primary dataset selector and click on lt Result gt This transfers the Result dataset to the Primary dataset for further process ing irt FS FID1 1 Re LL I fauatinegions 5 000 2 FID2 3 FID3 4 FID4 0 5 FIDS 10 000 5000 5 000 10 000 Intensity lama 2000 Time ns a e o e o aaa aaa sie fo 500 1 000 1500 Time ns Intensity J Figure 4 20 Original and baseline corrected datasets 9 10 11 12 Select the imaginary trace Click its viewport selec tion bar to activate it Repeat Steps 6
2. Li Timefns Close PulseSPEL Help Figure 4 6 Adjusting the Acquisition Trigger 4 6 BROKER i Acquiring a FID with the Pulse Tables An Additional Experiment 4 1 3 In order to demonstrate some of the artefact effects as well as show the relation of field offset and frequency we need to acquire an off resonance FID as well If you have followed the instruction in Section 4 1 2 proceed with the following steps 1 Shift the magnetic field 10 G higher Add 10 G to the Field Position value in the Field panel 10 000 5 000 5 000 10 000 0 500 1000 1500 2000 i Time ns Figure 4 7 An off resonance FID 2 Press the Run button 3 Save the spectrum E 580 User s Manual Acquiring a FID with PulseSPEL Acquiring a FID with PulseSPEL 4 2 As we have seen in Section 2 2 5 phase cycling suppresses the effects of offsets and imperfections in quad detection that may lead to artefacts In order to use the phase cycling we must use a PulseSPEL pulse program l 2 Follow instructions of Section 4 1 3 We want to have the magnetic field 10 G off resonance so that we can see any artefacts better Activate PulseSPEL Click the Run from PulseSPEL button in the Acquisition panel F7 EPR Parameters Pattems Field RF Acquisition l Scan Options ABSC
3. agPgload Group Contents of this Group PulseSPEL Program Path aredPulseSPEL Standard PulseSPELZ000 SPEL2 Create File echo_ir exp show Filenames 7 Load Cancel Help Load Button Figure 6 4 Selecting the PulseSPEL program Edit the PulseSPEL program The standard Puls eSPEL program needs a bit of modification to suit our needs so this is an excellent opportunity to learn how to modify pulse programs Make the changes indicated in Figure 6 5 The second highlighted section is a bit tricky The first line needs a semi colon at the beginning of the line to comment it out In the second line the x is replaced by a ph2 E 580 User s Manual Inversion Recovery with Echo Detection L ENE Ne Ne Ne Ne begin defs dim s 1024 1 end defs begin lists phi x asgl a bsgl b end lists r begin exp SPT QUAD L sweep x 1 to sx shot i 1 to h p2 ph1 d2 dx po x dl pl x do acq sgl next i dx dx d30 next x end exp Figure 6 5 r cho detected inversion recovery echo detected inversion recover begin defs dim s 1024 1 end defs r r begin lists end lists 7 7 begin exp SPT QUAD 7 x 1 to sx i l to h ph1 sweep shot p2 d2 dl pl x l O acq next i dx dx d30 next x sgl end exp Original left and modified right PulseSPEL programs for inversion recovery with echo detection Added and modified s
4. Figure 6 20 The PulseSPEL window 6 22 i Three Pulse ESEEM The PulseSPEL edi tor works very much like any standard text editor For details see Appendix D 5 Compile the variable definitions Click the Compile button See Figure 6 20 This compilation initializes all the various delays lengths and counters to the default values 6 Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file 2Dstd_set exp and click the Load button agPgload Group Contents of this Group m 4pulse_eseem2d ne racy PulseSPEL Program 2 Path aredPulseSPEL Standani PulseSPELZO00 SPEL2 Create File zDsta sete show Filenames Load Cancel Help Load Button Figure 6 21 Selecting the PulseSPEL program 7 Edit the PulseSPEL program The standard Puls eSPEL program needs a bit of modification to suit our needs so this is an excellent opportunity to learn how to modify pulse programs Make the changes indicated in Figure 6 23 Only one line needs to be added E 580 User s Manual 6 23 Three Pulse ESEEM Ne Ne Ne Ne Ne Ne Ne stimulated echo begin defs dim s 51 end defs T E begin lis 2 1 ts phl x x x ph2 x x X X xperiment Ne Ne Ne Ne
5. k Figure 2 50 The effect of bandwidth reduction on an FT EPR spectrum Note this does not effect fieldswept spectra E 580 User s Manual 2 47 Pulse EPR Practice The Pulse Programmer 2 2 2 In order to excite and detect FIDs and echoes many events must be orchestrated First because the TWT is a pulse amplifier it must be turned on a little before the microwave pulse The microwave pulse must be supplied to the TWT at a precise time after the TWT is turned on This pulse is produced by turning the x and pulse gate PIN diodes on and off at precisely the same time While the high power microwaves are on the defense diode must protect the preamp Lastly we must trigger the digi tizer to acquire the signal wr X Pulse Gate Defense Pulse Acquisition Trigger Figure 2 51 The timing for a pulse experiment The PatternJet pulse programmer supplies all the signals that orchestrate all the individual components so that each event W J A m a 2 48 i Pulse EPR Practice occurs precisely at the right moment It would be very difficult indeed if we had to determine all the delays and pulse lengths to perform each experiment This is why the Xepr software by default automatically calculates everything for us after calibra tion at the initial spectrometer installation All we have to supply are the time and length
6. 10 11 12 13 Insert the sample into the resonator Refer to Appendix A for details on mounting and changing sam ples Follow the resonator dip Use the frequency slider to center the resonator dip once more Realign the external stabilizer dip with the reso nator dip Overcouple the resonator Move the coupling adjust ment arm up See Figure 3 6 The resonator dip will become very broad i e overcoupling drops the resonator Q Adjust the frequency slider to keep the resonator dip centered Continue until the coupling adjustment arm is all the way up Realign the external stabilizer dip with the reso nator dip Microwave Bridge Tuning Frequency EELE r v Stand By Bias Kare Las gt v Operate Signal Phase a ZE p Auto Tuning ye v up v Fine man Re c v Down A Stop Reference Am ale ee von Off Dual Trace 7 Attenuation dB 120 0 Log Scale _ a H Options Iris Al yi Monitoring Qose Help Figure 3 8 Properly centered and overcoupled resonator dip with aligned external stabilizer dip 3 6 i Tuning Up 14 Switch to operate mode Click the Operate button See Figure 3 5 15 Center the Lock Offset indicator Readjust the fre quency slider until the Lock Offset indicator is centered Diode Current uA Lock re Pl Figure 3 9 The Lock Offset indicator 16 Turn the reference arm on Click the Refere
7. ERROR user in e680 Experiment ftEpr Patten exceeds shot repetition time x Q e680 Experiment acquisition aborted x i Figure 6 13 SRT error message In Step 7 we see that the total length of time required is greater than 2 ms because of the long time between the first two pulses The default value of SRT Shot Repeti Inversion Recovery with Echo Detection tion Time is 500 x 1 02 us We are attempting to repeat the experiment in a time shorter than the time required to perform the experiment To remedy the error set SRT to 2010 x 1 02 us or longer Variable Value d1 400 ns d2 400 ns d0 Determined in Step 14 of Section 6 1 1 d30 2 us pO 16 ns p1 32 ns p2 32 ns h 10 SRT 2010 x 1 02 us Table 6 3 Correct variable values for the inversion recovery experiment 10 Press the Run button Use the variable values given in Table 6 3 The spectrometer then acquires the inversion recovery and it appears in the viewport See Figure 6 14 This pulse program will go through the four steps of the phase cycle 11 Store the spectrum E 580 User s Manual 6 15 Inversion Recovery with Echo Detection Phase the data The imaginary data should be flat If you followed the directions in Section 5 2 correctly phasing should not be necessary If there is an appreciable amount of signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum unt
8. Slice v current ayy Operation vi vily Automatic Value Close Help Window Figure 5 7 Multiplying the spectrum by 1 15 Transfer the Result dataset to the Primary 16 dataset Fit a decaying exponential to measure T4 Click the Exponential Decay command in the Exponentials submenu of the Fitting subnenu The Exponential Decay dialog box appears Click the Fit button and the program will fit an exponential curve to your inversion recovery E 580 User s Manual Inversion Recovery with FID Detection The value Tau is the fitted T value it should be approxi mately 100 ns Exponential Decay Command Figure 5 8 Fitting an exponential to the inversion recovery 5 8 shg A Standing Hahn Echo A Standing Hahn Echo 5 2 This experiment measures the Hahn echo of a coal sample The word standing refers to that fact that the two pulse are held sta tionary This experiment acts as a setup experiment for the experiments in Section 5 3 and Section 5 4 We use the results to determine the Acquisition Trigger position and the best mag netic field for the future experiments We shall use two equal length 27 3 pulses separated by 400 ns The SpecJet then digi tizes the signal in transient digitizer mode 400 ns Data Acquisition Figure 5 9 The standing echo experiment 1 Follow the instructions in Chapter 3
9. Thermocouple Cable Figure A 1 The parts for a FlexLine resonator A 1 Waveguide SMA Transition Sample Rods Panna Semi rigid Cable i Sample Holders Woo aske D TTTT D Waveguide Screws ioe BROKER CoO Resonator Description Figure A 1 aids you in identifying the supplied parts for a Flex Line resonator Part numbers for the parts are given in Table A 1 Part Part Number Probehead Support ER 4118SPT Resonator Module ER 4118 xxx Waveguide SMA Transition ER 4118 1001 Semirigid Cable ER 4118 1000 Sample Rod ER 4118SR Sample Holders ER 4118SR P Waveguide Gasket ER 4102ST 1002 Waveguide Screws ER 4102ST 1018 Thermocouple Cable ER 4118 1010 8mm Wrench ER 4118 1007 1 4 Wrench ER4118 1008 2 5 mm Allen Wrench ER 4118 1009 Table A 1 Parts and part numbers for a FlexLine resonator For split ring resonators you will also find three additional items sample supports These supports look like white plastic screws with the central shaft drilled out See Section A 5 E 580 User s Manual A 3 Resonator Description The Probehead Support A 1 1 Sample Access Coupling Pa o Adj ustment leery Decreased Coupling Microwave Connector Thermocouple Connector Water Connections Modulation Connector Microwave Connector Thermocouple Figure A 2 Front and
10. i Using this Manual Typographical Conventions 1 1 2 Times Helvetica Courier Special notes A Warning box Hint box Special fonts are used in the text to differentiate between normal manual text and text displayed in the program This is the font used for the normal text in the manual This is the font used for text that is displayed by the program or must be entered into the program by you This is the font used for text in examples of PulseSPEL pulse programs 1 1 3 Some special notation is employed in this manual to simplify the descriptions The content between the brackets needs to be substituted with proper entries by the user The right bracket indicates sequential selection of the menu entries For example Processing gt Filtering gt Smoothing means clicking the Processing button in the menu bar followed by clicking Filtering in the sub menu and then clicking Smoothing You will see a warning box sometimes in the lefthand margin These are meant to point out critical information In particular it warns you about any procedures or operations that may be dan gerous to the spectrometer or you Always read and follow this advice In addition there are also hint boxes in the lefthand margin These are meant to be helpful hints and point out important information E 580 User s Manual Notes sD BROKER EPL Pulsed EPR Primer 2 This chapter
11. where Xx x lt x0 gt XW lt xmax gt lt x0 gt X Apply Cose Help Figure 7 20 The Hamming window dialog box E 580 User s Manual 7 17 The HYSCORE Experiment 22 23 24 Click the Slices All button This ensures that the Hamming window is applied to each of the slices of our two dimensional dataset If you do not perform this step you will receive an unpleasant surprise Your 2D dataset is converted into a 1D dataset Click the Apply button followed by the Close but ton The default values work well for this example Transfer the Result dataset to the Primary dataset After you click Close a dialog box appears asking if you want to Move result to input Click Yes Please decide Move result to input Figure 7 21 Transferring the Result dataset to the Primary 25 26 dataset Interchange the axis direction We are processing slices parallel to the t axis We need to process in the ty direction as well Click the interchange axis button Repeat Step 21 through Step 24 W J A m a i The HYSCORE Experiment 27 Select the 2D FFT command Click its button in the Transformations submenu of the Processing menu Diff amp integ Filtering z Algebra Peak Analysis Complex Window Functions Transformations F FFT Command im
12. Variable definitions are stored on the hard disk in files with the three letter def extension The standard values for the variable definitions are stored in a file called descr def Each PulseSPEL i e Spel1 Spel2 directory contains such a file Here is an example file PulseSPEL general variables definitions amp convention begin defs Feb 2000 Variables P EH r Comments po 16 90 pulse length p1 32 180 pulse length p2 32 p3 40 p7 80 LeCroy trigger p9 1000 pg 24 Integrator Gate Width do 40 data trigger offset time dl 200 Initial delay between the first two pulses d2 300 Initial delay between the second and third pulses d3 300 Initial delay between the third and fourth pulses d4 2000 d5 400 dx 0 t2 time scale starting value dy 0 tl time scale starting value C gt D 2 PROBER The PulseSPEL Programming Language i d30 4 t2 time scale increment d31 4 tl time scale increment d20 0 Initial value of dx d21 0 Initial value of dy i h 5 number of shots loop counter I n 20 number of sweeps to accumulate counter K s 300 Sweep length n of data really taken counter X t 1 second time axsis sweep length counter Y m 10 i srt 500 srtu shot repetition time srtu lusec r 1 s Cc 1 b 1 i w 800 Split point of
13. 17 Perform an experiment If you have successfully completed all of these steps it is safe to perform an exper iment Safety Test Figure 3 23 A FID that can be confused with ring down E 580 User s Manual 3 19 Changing Samples Changing Samples 3 4 Usually changing the sample requires only removing the old sample and inserting the new sample There are two exceptions to this rule The first is if you are running at temperatures below room temperature If this is the case you should consult Section A 3 for details In most cases you The second exception is if the samples differ greatly in size or can simply remove dielectric properties and therefore shift the resonator frequency the sample and insert substantially In that case we shall perform the steps in Pee Section 3 3 and Section 3 2 in almost reverse order to change samples 1 Press the Stop button This stops the pulse program mer FT EPR Parameters Pattems l Fed RF Acquisition Scan Options PULSE PATTERNS Channel Selection Acquisition Trigger 1 Sh Integrator Time Base ns Single Point y Stop Button Edit ETS Close PulseSPEL Help Figure 3 24 The Stop button 3 20 i Changing Samples A It is extremely important to deacti vate the HPP button first before the QUAD button is deactivated Per forming
14. ie T T T UFA A a T T f ae 0 500 1 000 li Time ns i a e ey ar ae a ae 1500 2 000 Figure F 8 Verifying equal pulse amplitudes among the four pulses E 580 User s Manual F 9 Phase amp Amplitude Adjustment Fine Adjustments F 3 The preceding procedure adjusts the amplitudes and phases fairly well There is however an ambiguity in the phases of the Y and Y pulses because we did not use quadrature detection Is the Y pulse 7 2 or 2 2 phase shifted from the X pulse The best way to test and verify the phase is to perform an actual experiment with the coal sample This experiment also allows you to adjust phases very precisely As was already mentioned in the introduction to this appendix it is critical to have the spectrometer well warmed up for these adjustments We shall use the nulled or out of phase signals in the adjustments and these signals are very sensitive to small fre quency and field drifts F 10 Phase amp Amplitude Adjustment 1 Follow the instructions of Section 5 2 Do not for get to turn Channel 2 of the SpecJet back on and recon nect the DS1 cable Take particular care to null the imaginary channel with the Signal Phase in the Micro wave Bridge Control window 1 500 2 000 0 Time ns Figure F 9 An echo from two X pulses properly phased and on resonance E 580 User s Manual F 11 Phase amp Amplitude Adjustment 2 Program tw
15. screw Transform SQRT of Abscissa Butt on Normalize Axes Figure 5 48 The FFT command 20 Click the Transform button The default options are appropriate for what we are doing The result will appear in the Primary dataset 7 7 7 7 T 0 06 0 04 0 02 0 0 019999 0 039999 0 059999 lt unnamed gt GHz Figure 5 49 Complex components of the ESEEM spectrum 5 42 5 i Two Pulse ESEEM 21 Select the Absolute button in the Complex sub menu of the Processing menu The software will calculate the magnitude spectrum of our complex data Processing Diff amp nteg Absolute Filtering Z Algebra 3 Command Peak Analysis Complex R Window Functions Absolute Transformations Power magin _ Real Part Fitting _ Imag Part Structure _ Re lt gt m XSophe Conjugate ProDeL v Buiki Complex Automatic 2 Figure 5 50 The Absolute command 22 Select the Normalize Axes command in the Transformations submenu of the Processing menu GHz is not the most sensible unit for ESEEM This command converts it to the more sensible MHz Processing Diff amp Integ Filtering 2 Algebra Peak Analysis r Complex td Window Functions imagini Z Zero Fiting Fitting T Transformation Structure _ FFT Real XSophe 2D FFT Submenu pct Cross Term Averaging
16. 6 Set the Shoots Per Loop This value specifies the number of times the Figure 5 18 signal is averaged Set it to 10 See E 580 User s Manual 5 17 Echo Detected Field Swept EPR 7 Select a Magnetic Field scan Select Magnetic Field as the X Axis Quantity in the Acquisition panel X Axis Quantity Window Field l RF TITIES AND SIZES pae Acquisition l Scan l Options tity Time al Pme om e RF2 EIE with RFI Run from Tq EIE with RF2 Run from X Axis Size Window X Axis Size 1024 Y Axis Siz ALE Tables Button Phase Cycling y Phase Program Normal y Gose PulsesPEL nep Figure 5 19 The Acquisition panel 8 Set the X Axis Size Set the value to 1024 See Figure 5 19 Select Run from Tables Verify that the Run from Tables option is selected in the Acquisition panel i Echo Detected Field Swept EPR 10 Set the Sweep Width to 100 G Sweep Width Window Figure 5 20 Setting the Sweep Width 11 Set the Center Field The present Field Position is still the value that brought our signal into resonance Enter this value into the Center Field box E 580 User s Manual 5 19 Echo Detected Field Swept EPR Press the Run button See Figure 5 5 The spec trometer then acquires the field swept spectrum and it appears in the viewp
17. XSophe 2D FFT Submenu ProDeL Cross Term Averaging Automatic Convolitian undo Deconvolution 4 Normalize Axes Command Symmetnization Invert Abscissa g Factor SQRT of Abscissa Normalize Axes Figure 7 24 The Normalize Axes command 7 20 The HYSCORE Experiment 31 Interchange the axis direction We are processing slices parallel to the t axis We need to process in the ty direction as well Click the interchange axis button 32 Repeat Step 30 33 Click the 1D 2D button The ESEEM spectrum will appear in the viewport as a density plot 1D 2D Button ports Properties Options BRUKER Xepr File Acquisition Processing Be e 4 ee Figure 7 25 Changing to a 2D display 34 Click the Display Range command in the Proper ties menu Enter 0 in the x Min box Click Set and then Close See Figure 7 27 vpRange x Min i x Max sezs0s77 5 y Min EE y Max 81 005659 Figure 7 26 The Display Range dialog box E 580 User s Manual 7 21 The HYSCORE Experiment Figure 7 27 A HYSCORE density plot The ridges intersecting the diagonal at approximately 15 MHz are the proton signals and the ridges at about 3 5 MHz are due to natural abundance 3C 7 22 ope FlexLine Resonators A This appendix describes the use of the Bruker FlexLine series resonators All the
18. E 580 User s Manual Inversion Recovery with Echo Detection Inversion Recovery with Echo Detection _ 6 1 In this section we shall measure the T spin lattice relaxation time of the coal sample As we discussed on page 2 38 three microwave pulses produce five echoes In order to suppress the unwanted echoes we shall use a PulseSPEL program using the phase cycle shown in Figure 6 1 X X X A B X x x A B C D X X X Cc X X X D Figure 6 1 A phase cycle to eliminate unwanted echoes in an inversion recovery experiment i Inversion Recovery with Echo Detection The Inversion Recovery Setup Experiment 6 1 1 1 Follow the instructions of Section 5 2 Follow the steps up to and including Step 13 2 Activate PulseSPEL Click the Run from PulseSPEL button in the Acquisition panel FTEPR Parameters Patterns Field RF Acquisition l Scan l Options l ABSCISSA QUANTITIES AND SIZES X Axis Quantity Time x X Axis Size 1024 E Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables Run from PulseSPEL Quadrature Detection E a aa Run from PuisesPeL Pod PulseSPEL even Button a ees PulseSPEL Mead ee y Button y ose PulseSPEL Help Figure 6 2 The Run from PulseSPEL button E 580 User s Manual Inversion Recovery with Echo Detection Load Var Def But
19. We know from the convolution theorem that the time domain signal is simply the product of the two transformed functions See Equation 2 26 We already know the Fourier transform for a lorentzian t T a 2 27 Next we have to calculate the Fourier transform of the three line stick spectrum One thing that helps is that this signal is symmet ric yielding a purely real time domain signal Using the additive properties of Fourier transforms we express the three line stick spectrum as the sum of two signals with known Fourier trans forms Adding the two time domain signals gives us the Fourier transform of the stick spectrum pb m na I i th cos At 4 1 cos At Figure 2 27 The Fourier transform of a three line stick spec trum obtained as the sum of two functions Q nn i 7 Multiplying the two time domain functions gives us the result in Figure 2 28 This is the FID of the three line EPR spectrum CUE b Nod Figure 2 28 FID ofa three line EPR spectrum 2 30 Pulse EPR Theory On this and the next page are examples of what happens to the FID when the EPR signal changes j Q J As the linewidth of ad cad el a the EPR signal increases the FID decays more quickly f t BN a p a Figure 2 29 The effect of linewidth F o r LU ook As the splitting of a the EPR
20. asgl ta a a a bsgl b b b b end lists begin exp SPT QUAD A sweep x 1 to sx shot i 1 to h pO ph1 dl pO ph2 d2 po x do dx acq sgl next i dx dx d30 next x end exp program to evaluate timing and phases dimension of data array sx sy phase program for 1st pulse phase program for 2nd pulse sign program for RE part sign program for IM part single point detection lst pulse and phase progr constant pulse separation 2nd pulse and phase progr constant pulse separation 3rd pulse in x channel initial acquisition delay increment acquisition delay Figure 6 22 Original PulseSPEL programs for a stimulated echo setup experiment 6 24 Three Pulse ESEEM stimulated echo experiment program to evaluate timing and phases Ne Ne Ne Ne Ne Ne Ne begin defs dim s 512 1 dimension of data end defs r begin lists phl x x x x ph2 x x Xx X asgl a a a a bsgl b b b b end lists phase program for phase program for Ne Ne Ne Ne sign program for I A r begin exp SPT QUAD single point detec r sweep x 1 to sx shot i l to h sign program for R array sx sy lst pulse 2nd pulse E part part tion pO ph h1 lst pulse and phase progr d1 constant pulse separation pO ph2 2nd pulse and phase progr d2 constant pulse separation po x 3rd pulse in x channel a initial acquisiti
21. Left Right Shift Polar to Rect Rect to Polar Linear Figure 4 21 The Left Right Shift command 4 18 ekGaen Processing the FID 2 Shift the data to the left Enter a number in the Points box and click the Shift button Negative values shift the A Qy data to the left Continue until the first point of the FID Q after the deadtime is at the left edge of the viewport Click the Close button and then the Yes button in the dialog We already have a box that appears The result is now transferred to the Pri good guess for the mary dataset number of points The delay in Section 4 1 2 was la psan Points Box about 528 ns with 4ns per point Therefore 528 4 132 is a good start ing point Slice current v Please decide Points 132 Mode shift v circulate Move result to input lt distance gt is in abscissa units negative values mean left shift joe cose Help Shift Close Button Button Figure 4 22 The Left Right Shift dialog box Button 10000 5 000 5 000 10 000 0 500 1 000 1 500 2 000 a Time ns Figure 4 23 A properly shifted FID E 580 User s Manual 4 19 Processing the FID FFT 4 3 3 After all the preprocessing we can finally use the FFT
22. Validate the PulseSPEL program Click the Vali date button The pulse program is not only compiled but also each step is checked to verify that it is within the lim its of the spectrometer capabilities If successful the state ment Second pass ended appears in the message window Close the PulseSPEL window Double click the close button Acquisition Ent k Trigger oe gt d1 dx d1 d0 dx Figure 5 39 Definition of the variables for echodecay 2phi exp Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 5 34 Set the variables to the values indicated in Table 5 2 5 36 W J A m a Two Pulse ESEEM Variable Value d1 88 ns do Top of echo determined in Step 12 of Section 5 5 1 d30 8 ns pO 16 ns p1 32 ns h 100 n 1 Table 5 2 Variable values for the ESEEM experiment T Press the Run button The spectrometer then acquires the echo decay and it appears in the viewport This pulse program will go through the two steps of the phase cycle T T T T T T 0 500 1000 1500 2000 2500 3000 3500 4000 Time ns Figure 5 40 ESEEM of the coal sample E 580 User s Manual 5 37 Two Pulse ESEEM Save the spectrum Phase the data The real data should be an exponential decay See Figure 5 40 and the imaginary data should be flat If you followed the directions
23. a p p If the lengths are not exactly divisible the patterns must be repeated until each patterns is repeated an integral number of times For example begin lists pho x phl x x ty asgl ta a bsgl b b end lists is equivalent to begin lists PNO x x X k X x phil x x y x x Yy asgl ta a ta a a a bsgl b b b b b b end lists The actual commands used to perform a pulse experiment are in the experiment section of the pulse program It starts with a begin exp statement and ends with an end exp statement for example begin exp QUAD SPT various commands end exp The begin exp statement is followed by options delimited by square brackets Valid options are QUAD Quadrature is used If Quad is not selected only the first quadrature detec tion channel is acquired SPT Use the SpecJet in single point mode E 580 User s Manual D 7 The PulseSPEL Programming Language TRANS Use the SpecJet in transient recorder mode INTG Use the SpecJet in integrator mode Commands and Operations D 1 3 Delays Pulses Delays are variables that define the time between events Events are defined as microwave pulses and trigger pulses for acquisi tion or external devices The variable values delay lengths can be defined in the variable definitions file in the program through algebraic operations and via editing in the Acquisition panel of the F
24. amp integ Filtering r Algebra Peak Analysis Complex FFT Command Window Functions Symmetrization Invert Abscissa g Factor Transform SQRT of Abscissa Button Normalize Axes Figure 6 38 The FFT command 22 Click the Transform button The default options are appropriate for what we are doing The result will appear in the Primary dataset 0 03 0 02 001 oO 0 01 0 019999 0 03 Figure 6 39 Complex components of the ESEEM spectrum 6 38 ip Three Pulse ESEEM 23 Select the Absolute button in the Complex sub menu of the Processing menu The software will calculate the magnitude spectrum of our complex data Processing Diff amp Integ Absolute Filtering Z Algebra 3 Command Peak Analysis Complex Window Functions Absolute Transformations Power maging _ Real Part Fitting _ Imag Part Structure _ Re lt gt m XSophe Conjugate ProDeL e Buiki Complex Aurtamatic 2 Figure 6 40 The Absolute command 24 Select the Normalize Axes command in the Com plex submenu of the Processing menu GHz is not the most sensible unit for ESEEM This command con verts it to the more sensible MHz Processing Diff amp Integ a Filtering Algebra Peak Analysis Complex r Window Functions sformations maging
25. dx d30 next x This program will run more slowly than a sweep loop because the PatternJet controls the loop in hardware when a sweep loop is used Only one set of instructions needs to be sent for a sweep loop whereas a for next loop would require reprograming the PatternJet for each iteration of the loop Because the PatternJet reprograming can be the rate limiting step in an acquisition there are unusual cases where the variable SRT does not control the experiment repetition rate The first requirement for this unusual case is a Shot loop with limits from 1 to 1 within a for next loop The second requirement is the use of an acq command or a dig command with No of Aver ages set to one on the SpecJet If these two conditions are both true the repetition time is usually determined by the PatternJet reprograming time For a simple program this is about 0 5 sec onds If SRT is greater than the PatternJet reprograming time then the repetition rate is determined by SRT E 580 User s Manual D 12 The PulseSPEL Programming Language Any general variable can be used for the loop counter as well as the loop limits For next loops are often used for 2D acquisi tions for y 1 to sy dx 0 sweep x 1 to sx Shot i g toh some commands next i dx dx d30 next x dy dy d3l next y Bsweep The next type of loop sweeps the magnetic field The range of field values is determined by the Center Fiel
26. p2 p0 you can accomplish it as follows a p2 pod pl p3 al There are a number of loop structures in PulseSPEL The one that must be used in every program is the shot loop It triggers the PatternJet to produce its pulse pattern The repetition rate of this loop is determined by the variable SRT Shot Repetition Time Within a shot loop no change of pulse and delay variables is allowed The general structure is as follows Shot i g toh some commands next i Any general variable can be used for the loop counter i as well as the loop limits g and h You can also use integers for the loop limits If an acq statement is used the number of averages per formed in this loop is h g If a dig statement is used the number of averages is controlled by the SpecJet The shot loop does not allow changes in any pulse lengths or delays In order to program a loop in which these quantities can be changed a sweep loop is used The loop variable must be x In this example we increase the delay variable dx by steps of d30 D 10 The PulseSPEL Programming Language For Next Loops sweep x e to f Shot i g toh some commands next i dx dx d30 next x A third type of loop is the for next loop which is similar to looping structures in a number of programming languages We could have programmed the previous example in the following manner for x e to f Shot i g to h some commands next i dx
27. 2nd pulse and phase progr d2 constant pulse separation po x 3rd pulse in x channel do initial acquisition delay dx increment acquisition delay acq sgl next i Message Window a pi E pa Loaded file fusr people rtw xeprFiles Pulse SPEL shared Pulse SPEL Standard Pulse SPEL2000 SPEL272D Figure 6 24 Validating the PulseSPEL program 9 Close the PulseSPEL window Double click the close button 6 26 ioe BROKER CoO Three Pulse ESEEM pO NIA pO NIA pO Nia Acquisition Trigger d2 d1 Figure 6 25 Variable definitions for the modified 2Dstd_set exp 10 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 6 26 Set the variables to the values indicated in Table 6 4 Variable d1 d2 do d30 pO h Value 240 ns 400 ns 0 ns 4 ns 16 ns 10 Table 6 4 Variable values for the setup experiment E 580 User s Manual 6 27 Three Pulse ESEEM PulseSPEL Variable Box Figure 6 26 Editing PulseSPEL variables 11 Increase the HPP attenuator by 1 dB We optimized the microwave power for two 27 3 pulses in Section 5 2 Here we need the 16 ns pulse to be a 2 2 pulse 12 Press the Run button The spectrometer then acquires the stimulated echo and it appears in the viewport This pulse program will go through the four steps of
28. Experiment Button Tuning Button SpecJet Button Figure 3 4 Important buttons for pulse operation E 580 User s Manual 3 3 Tuning Up 2 Switch to tune mode Click the tune button Frequency Microwave Bridge Tuning Adjustment Bias Tune Button p rme Adjustment bel a wv Stand By Bias Tune palate aa v Operate Signal Phase Reference lt lt ERE Arm Buttons K AA Operate P baie e v Down A Stop Referen Button v On off Attenuation dB Dual Trace 7 ct ew Log zJ pa Zi Dual Trace Button Ajy Monitoring A Attenuator M Adjustment ad pne Figure 3 5 The microwave bridge tuning dialog box 3 Set the CW attenuator to 20 dB The external stabi liz r i required 4 Turn the reference arm off Green indicates that the because the resona button is activated Click the Reference Arm Off button tor has a very low Q so that it is green se ee res 5 Click the Dual Trace button Two traces will appear time Therefore the in the display One trace is the external stabilizer trace that AFC cannot lock to is used to lock the microwave source frequency It is the resonator dip Instead we tune the external stabilizer to the resonator fre quency and lock on the stabilizer dip inverted i e the dip will go upwards
29. Load Button File hyscoresetexp show Filenames Figure 7 5 Selecting the PulseSPEL program groan Cancel Help Q 7 Edit the PulseSPEL program The standard Puls eSPEL program needs a bit of modification to suit our ee d needs Make the change indicated in Figure 7 6 tor works very much like any standard text editor For details see Appendix D The HYSCORE Setup Experiment begin defs dim s 256 1 end defs r begin lists phl x x xX X ph2 x x x Xx asgl a a ta a bsgl b b b end lists L r begin exp SPT QUAD dx 0 dy 0 p2 ph1 pO ph2 dx acq sgl next i dx dx d30 next x dx 0 end exp begin defs dim s 256 1 end defs r begin lists phi x x x Xx ph2 x x x X asgl ta a ta a bsgl b b b 5 end lists A li begin exp SPT QUAD r dx 0 dy 0 sweep x 1 to sx shot i 1 to h po x d1 po x d2 p2 phi d3 pO ph2 e dod dx acq sgl next i dx dx d30 next x dx 0 end exp Figure 7 6 Original left and modified right PulseSPEL programs for HYSCORE setup Added and modified sections are highlighted E 580 User s Manual 1 5 The HYSCORE Setup Experiment Close Button Validate Button Figure 7 7 Validate the edited PulseSPEL program Click the Validate button The pulse program is not only compiled but also each step is checked
30. ment Second pass ended appears in the message window 5 32 Field Sweeps with PulseSPEL 4 Close the PulseSPEL window Double click the close button Integrator po p1 Gate H d1 d1 0 pg Figure 5 36 Definition of the variables for echo_fs exp 5 Set some PulseSPEL variable values We have already set most of the variables in the previous section What remains are the Acquisition Trigger delay dO and the width of the integrator gate pg Using the values you recorded in Step 12 of Section 5 5 1 set pg to the width of the echo and dO to dO echo top echowidth 2 5 2 6 Set the Sweep Width to 100 G This is sufficiently wide to capture the whole EPR spectrum of the coal sam ple We already determined the Center Field in Section 5 2 7 Press the Run button The spectrometer then acquires the echo detected field swept EPR spectrum and it E 580 User s Manual 5 33 Field Sweeps with PulseSPEL appears in the viewport This pulse program will go through the two steps of the phase cycle S SS eae e EA 3390 M0 W0 MWA MW M40 3M5 MO WO MO Field G Figure 5 37 A field swept echo detected EPR spectrum 8 Save the spectrum 9 Phase the data The real data should be an EPR absorp tion spectrum See Figure 5 37 and the imaginary data should be flat If you followed the directions in Section 5 2 correctly phasing should not be necessary If there is an appreciable a
31. mysterious error message Attention ERROR user in e680 Experiment ftEpr Maximum gate time of TWT exceeded e680 Experiment acquisition aborted ox se Figure 6 12 TWT gate length error message E 580 User s Manual 6 13 Inversion Recovery with Echo Detection In Figure 2 51 we see that a pulse is needed to turn the TWT on With d2 96 ns both the first and second micro wave pulses are so close together that they must share one TWT gate The maximum time that the TWT can be turned on or gated is 10 ps At the end of our experiment the microwave pulses are 1024 number of points x 2 us time increment 96 ns initial value gt 2 ms apart from each other which far exceeds the 10 us limit One solution is to have two TWT gates one for each pulse Then no matter how far apart the pulses are the TWT gate time remains small and constant The TWT also requires a minimum time between the TWT gates before the soft ware will program two separate TWT gates This mini mum time between two microwave pulses that allows two separate TWT gates is usually about 300 ns We can rem edy the error by programming an initial d2 value of 400 ns so the software forces individual gates for the two microwave pulse 8 Press the Run button The spectrometer attempts to acquire the inversion recovery 9 Heed the error message We receive the following mysterious error message Attention
32. p2 32 ns h 5 ee Table 7 1 Variable values for the setup experiment E 580 User s Manual 7 7 The HYSCORE Setup Experi ment FT EPR Parameters Pattems Field ABSCISSA QUANTITIES AND SIZES X Axis Quantity Time x X Axis Size 512 4 Y Axis Quantity Magnetic Field y Y Axis Size 1 IO Acquisition l Scan Options ACQUISITION MODE v Run from Tables Run from PulseSPEL v Read Transient v Start Transient Quadrature Detection 7 PulseSPEL Variable Box PulseSPEL ACQUISITION PulseSPEL Program SPEL2 fidcycle_bcstep exp PulseSPEL Variable d0 40 ns Experiment EXP y Phase Cycling LISTS y Phase Program Normal y PulseSPEL Help Figure 7 9 Editing PulseSPEL variables 11 Press the Run button The spectrometer then acquires the inverted echo and it appears in the viewport This pulse program will go through the four steps of the phase cycle Save the spectrum Repeat Steps 10 through 12 with p2 values between 26 and 38 ns Choose the pulse length that inverts the echo the most Record this number some where We shall use this value for p2 in the next section i The HYSCORE Setup Experiment 14 Find where the echo bottom is Place your cursor on the dataset and determine from the readout at what time the bottom of the inverted echo occurs See Figure 7 10 Record
33. performing a safety check It also describes how to shut the spectrometer down A demonstration of how to acquire FIDs Free Induction Decays using both the pulse tables and a PulseSPEL program You are also introduced to phasing spectra E 580 User s Manual Using this Manual Chapter 5 Chapter 6 Chapter 7 Appendix A Appendix B Appendix C Appendix D Appendix E Appendix F Appendix G A description of two pulse experiments such as inversion recov ery with FID detection and two pulse echo experiments Echo detected field swept EPR spectroscopy is introduced as well as Tm and ESEEM Electron Spin Echo Envelope measurements An explanation of three pulse experiments such as inversion recovery with echo detection and three pulse ESEEM It includes a two dimensional experiment A description of the four pulse 2D ESEEM experiment HYSCORE A manual on the use and care of FlexLine resonators A brief description of Nyquist issues as well as timing concerns when using the SpecJet digitizer in integrator mode A definition of the maximum number of pulses that can be pro grammed for the PatternJet A description of the many elements of the FT EPR Parameters panels The PulseSPEL Reference Manual PulseSPEL is the pulse pro gramming language for the Bruker E 580 spectrometer An explanation of the FT EPR configuration tables Procedures for adjusting microwave pulse phases and ampli tudes
34. x acq sgl AL next i do dx dx d30 e next x acq sg1 next i end exp dx dx d30 next x end exp Figure 6 10 Original left and modified right PulseSPEL programs for inversion recovery with echo detection Added and modified sections are high lighted E 580 User s Manual 6 11 Inversion Recovery with Echo Detection 3 Validate the edited PulseSPEL program Click the Validate button The pulse program is not only compiled but also each step is checked to verify that it is within the limits of the spectrometer capabilities If successful the statement Second pass ended appears in the message window 4 Close the PulseSPEL window Double click the close button p2 po p1 Acquisition Trigger z pS T 2 T d2 dx d1 d1 do Figure 6 11 Variable definitions for the modified echo_ir exp 5 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 6 8 Set the variables to the values indi cated in Table 6 1 Note that d30 is in units of microsec onds Inversion Recovery with Echo Detection Variable Value d1 400 ns d2 96 ns d0 Determined in Step 14 of Section 6 1 1 d30 2 us pO 16 ns p1 32 ns p2 32 ns h 10 Table 6 2 Variable values for the inversion recovery experiment 6 Press the Run button The spectrometer attempts to acquire the inversion recovery 7 Heed the error message We receive the following
35. Aligning the module and the semi rigid cable 6 Tighten the four 3x10 mm screws with the 2 5 mm Allen wrench See Figure A 17 J Press the module inner structure in until the SMA connectors meet See Figure A 20 Figure A 20 Pushing the connectors together A 22 C gt BROKER CoD Changing Resonator Modules 8 Firmly yet gently tighten the male SMA connec tor with the 8 mm wrench Prevent the female con nector from moving with the 1 4 inch wrench 9 Insert the thermocouple into its hole in the mod ule Neatly arrange the thermocouple wires and hold the The SMA connector wires with the cable restraints See Figure A 15 and must be tight i e Figure A 16 you need a wrench to ae loosen the connec 10 Attach the modulation wires to the modulation tions but do not A overtighten ihe SMA pins Push the connectors onto the pins Neatly arrange Sicha Over the thermocouple wires and hold the wires with the cable tightening will either restraints See Figure A 15 and Figure A 16 cause reflections or worse yet break the SMA connector Use of an SMA torque wrench ensures proper tightening E 580 User s Manual A 23 Sample Supports for Split ring Resonators Sample Supports for Split ring Resonators A 5 If you use your split ring resonator for CW experiments you will need to use sample supports They function almost like the pedestal in a standard cavity it prevents
36. Automatic Convolition undo Deranvolition iy J Symmewzaton Normalize mop enana Axes Command g Factor SQRT of Abscissa Normalize Axes Figure 5 51 The Normalize Axes command E 580 User s Manual 5 43 Two Pulse ESEEM 23 Select the Display Range command in the Prop erties menu Enter 0 for X Min The spectrum is sym metric so we only need to look at positive values Properties Display Range X Min fei ee Window Display Range vpRange Command x Min 32 497559 i 1D Sieg Positien 2D Level urve 2B rve Center 20 Caler Seheme 20 Projection Type 2B Perspective y Min 5 9543357 2 y Max 366 31568 2 Figure 5 52 The Display Range dialog box Figure 5 53 A magnitude ESEEM spectrum ip Advice for Real Samples Advice for Real Samples 5 7 The very strong signal of the coal sample makes it very easy to adjust the acquisition trigger magnetic field HPP attenuator set ting and signal phase How is it possible to accomplish all of this with a very weak signal with which we need to perform extensive signal averaging In most cases the parameters such as timing and microwave power do not change greatly from sample to sample Other parameters such as Signal Phase can be corrected after the acquisition with the data processing soft ware If you keep records of your PulseSPEL variables and HPP
37. Bruker pulse resonators as well as many of the L and S band resonators are based on this design One char acteristic they all have in common is the small size of the reso nator itself Unlike the more standard Bruker cavities in which the cryostat is inserted inside the cavity and only the sample is cooled the FlexLine resonators must be inserted into the cry ostat because a cryostat will not fit in the small resonators As a consequence both sample and resonator are cooled or warmed for variable temperature operation In most cases the cryostat is used to mount the resonator in the magnet Sample exchange is convenient even at low temperatures by means of a sample rod and sample holders which grasp the sample tube Bruker designed the resonators for both CW Continuous Wave and pulse experiments The coupling range of the resonator is very large to achieve the very low Qs required for pulse work as well as the matched condition required for CW work Connec tions to the bridge are via semi rigid coaxial cables One of the unique and flexible features of the FlexLine Series is the interchangeable resonator modules The resonator consists of an upper portion call the probehead support and a lower portion call the resonator module Only one support is required even if you have many different modules E 580 User s Manual Resonator Description Resonator Description Probehead Support Resonator Module
38. Cancel Help Load Button Figure 5 31 Selecting the PulseSPEL program 5 28 i Field Sweeps with PulseSPEL Validate the PulseSPEL program Click the Vali date button The pulse program is not only compiled but also each step is checked to verify that it is within the lim its of the spectrometer capabilities If successful the state ment Second pass ended appears in the message window Close Button Validate Button Help On Selection PulseSPEL Programming Panel echo2phi exp edited dir usripeopleirtwixeprFiles PulseSPELisharedPuis File Edit Search Compile Properties Options standing echo program to evaluate timing for 2 pulse echo experiment two step phase cycle to eliminate FID after 2nd pulse begin defs dim s 512 1 dimension of data array sx sy end defs begin lists phi x x phase program for 1st pulse asgl a a sign program for RE part bsgl b b sign program for IM part end lists begin exp SPT QUAD Single Point QUAD detection for k 1 ton averaging loop sweep x 1 to sx sweep loop shot i 1 to h accumulation loop po phi A 1st pulse and phase program dl tau pl x 2nd pulse dl tau do constant acquisition delay dx increment trigger position acq sg1 ition next i accumulation loop dx dx d30 Message nt trigger position by d30 usar Window jeep toop Second pass ended EJ
39. Echo Echo 4 2 J Echo 0 2t t 2t 2t 2t t 2t 21 1 1 Figure 2 40 Echoes and timing in a three pulse experiment Remembering our Fourier theory broad in the time domain means narrow in the frequency domain The stimulated echo is particularly important because it also exhibits ESEEM effects when t is varied A Hahn echo decays with a time constant of T 4 2 whereas the stimulated echo decays with a time constant of approximately T Spin and spectral dif fusion contributions causes the stimulated echo to decay some what faster than T4 Ty is often much shorter than T so the ESEEM decays more slowly in a stimulated echo than in a Hahn echo experiment Therefore a three pulse ESEEM experiment usually gives superior resolution than a two pulse ESEEM experiment 2 38 Pulse EPR Theory Pulse Lengths and Bandwidths In Pulse EPR spectroscopy we often can excite only a small por tion of our EPR spectrum This fact simplifies things when per forming echo experiments First if we have a very broad EPR spectrum within the range of our excitation of the spectrum it looks almost flat and therefore approximately symmetric As a consequence our echo will be purely real with no imaginary component Second the echo width is approximately equal to the pulse width Quite often it is more convenient to use two equal length pulses instead of the traditional 7 2 m pulse sequence The reason for doing this
40. Gabe aan et ee Subtract Line Subtract Line Button Figure 6 33 The polynomial baseline fitting task bar Click the Slices All button This ensures that the base line subtraction is performed on each of the slices of our two dimensional dataset If you do not perform this step you will receive an unpleasant surprise Your 2D dataset is converted into a 1D dataset 12 prFitSquare Slice v current gt all Ft Function y ax 2 bx c Figure 6 34 The 2nd Order dialog box E 580 User s Manual 6 35 Three Pulse ESEEM 14 Subtract the baseline Click the Subtract Line button in the task bar The subtraction result appears in the result dataset Transfer the result to primary Click the Primary dataset selector and click on lt Result gt This transfers the Result dataset to the Primary dataset for further process ing Click the Return button See Figure 6 33 Click the Window Function task button The Win dow Function task bar then appears TASKS Baseline Correction Peak Picking Integration Fitting Window Function Filtering XSophe Save Status Window Function Button WINDOW FUNCTIONS Start Gai CE pine Sell PRSE DETSE ates CEEE aS Hamming Function Button Ere SE FFT lt GLE Figure 6 35 The Window Function task bar 6 36 i Thr
41. Pulse ESEEM Extract the real part of the dataset Once properly phased only the real part of the dataset contains the infor mation we seek Click the Real Part command of the Complex submenu of the Processing menu Figure 6 31 Processing Diff amp Integ Filtering Algebra r Peak Analysis Complex aaas Window Functions Absolute Transformations Power fraginy Real Part Fitting mag Part Structure Z XSophe ProDeL B Automatic The Real Part command Real Part Command 10 Click the Baseline Correction task button fol lowed by the Polynomial task button The polyno mial baseline correction task bar then appears Baseline Correction Button TASKS jaseline Correction Peak Picking Integration Fitting Window Function Filtering XSophe Sea Button Polynomial BASELINE Polynomial Spline Retum Figure 6 32 Selecting polynomial baseline correction 6 34 Three Pulse ESEEM A y The exponential decay is so slow that a second order poly nomial approxi mates the echo decay fairly well 11 Fit a second order polynomial to the baseline Click the Oth Order button in the task bar A fitted func tion appears Define Region Button Return Button BASELINE POLY Start Define Region 2nd Order C Baton me aha Ch COENE eee Ses
42. Run button You can then store or save your dataset You must have the pulse programmer already running to acquire a dataset in this mode Click the Start button next to the pulse tables in the Patterns panel first When you click the Run but ton the dataset acquired by the SpecJet will be transferred into the Primary dataset of the active viewport Quadrature Clicking this button toggles the Quadrature Detection on and Detection off Green indicates it is on PulseSPEL Acquisition C 4 3 See Appendix D E 580 User s Manual C 11 The Scan Panel The Scan Panel C 5 Figure C 10 The Scan panel Auto Scaling Turns Auto Scaling on and off When on the viewport display will be rescaled so the dataset is completely in view Replace Mode Turns Replace Mode on and off When off the signal is aver aged When on the present signal replaces the previous signal resulting in no averaging Averages Per Equivalent to Shots per Point in the Patterns panel Scan C 12 BRORER The Scan Panel Number of Scans Scans Done Accumulated Scans The number of scans to be acquired This parameter differs from Shots per Point described on page C 2 The acquisition control of these two parameters can best be described as two nested loops in a computer program For j 1 to Number of Scans Shot i 1 to Shots per Point Average spectrum next i Display averaged spectrum next j The number of average
43. SPEL2 Create File esrar def 1 show Filenames Load Cancel Help Load Button Figure D 4 The PulseSPEL window 4 Compile the variable definitions Click the Compile button See Figure D 4 This compilation initializes all the various delays lengths and counters to the default values D 24 Setting up a PulseSPEL Experiment Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and path You need to navigate to the desired path Select the desired file and click the Load button Load Program Button Figure D 5 t A a N NNNMNN PulseSPEL Programming Panel deser def dir lusripeopleirtwieprFilesiPulseSPEL sharedPuiseSPEL Stand File Edit Search Compile Properties Options PulseSPEL general variables definitions amp convention Feb 2000 PE Comments 16 90 pulse length 2 Baa Group Contents of this Group C a a T T a 0 o PulseSPEL Program Path JsredPulseSPEL Standard Pulse SPELZ000 SPELZ Create d30 4 mae File fucycte_bestep exp J show Filenames 0 0 Cancel E er of sweeps to accumulate Sweep length n of data really taken Help counter K counter X In 20 Button 6 Selecting the PulseSPEL program Validate the PulseSPEL program Click the Vali date
44. This microwave sig nal generated in the resonator is called a FID Free Induction Decay A 7 2 pulse maxi mizes the magnetiza tion in the x y plane z z and therefore maxi mizes the signal S rA x Rotating Lab Frame Frame Figure 2 8 Generation of a FID lt _ M Figure 2 9 Rotation of the magnetization acting like a gen erator 2 10 opGier Pulse EPR Theory Off Resonance Effects So far we have been dealing with exact resonance conditions i e the Larmor frequency is exactly equal to the microwave fre quency EPR spectra contain many different frequencies so not all parts of the EPR spectrum can be exactly on resonance simultaneously Therefore we need to consider what happens to the magnetization when we are off resonance First we shall look at the rotating frame behavior of transverse magnetization having a frequency following a 7 2 pulse Ini tially the magnetization will be along the y axis however because Wg the magnetization will appear to rotate in the x y plane This means that the magnetization either is rotating faster or slower than the microwave magnetic field B4 The rotation rate will be equal to the frequency difference A O OQ 2 5 In the case of Aw 0 the rotation rate is zero i e stationary which is precisely what we would expect for a system exactly on resonance If Aw gt 0 the magnetization is gaining and will rotate in a c
45. _ Zero Filling Fitting _ FFT Transformation Structure cs Reel XSophe 2D FFT Submenu ProDeL Cross Term Averaging Automatic tonvoltticn a 4 Deconvolution 4 Symmetrization Normalize Invert Abscissa Axes C ommand g Factor SQRT of Abscissa Normalize Axes Figure 6 41 The Normalize Axes command E 580 User s Manual 6 39 Three Pulse ESEEM 25 Click the 1D 2D button The ESEEM spectrum will appear in the viewport as a density plot 1D 2D Button ports Properties Options BRUKER Xepr File Acquisition Processing G16 G4 Pal Figure 6 42 Changing to a 2D display E Fs v EC EE 5 00 seconsary gt EI ro Rosa Ee aer 500 3500 450 p 3 000 L 400 k 2 500 350 L 2 000 1 500 1 000 H500 mo Viewport 1 Primary lt unnamed gt MHz Intensity Figure 6 43 A 2D ESEEM density plot 6 40 ioe BROKER CoO Three Pulse ESEEM The signal at approximately 15 MHz is a proton signal and the signal at about 3 5 MHz is due to natural abundance BC Notice the tau dependent oscillation of the signals This is the well known tau suppression effect E 580 User s Manual 6 41 Notes 6 42 HYSCORE 7 The HYSCORE HYperfine Sublevel CORrElation is a four pulse two d
46. a x pulse the x PIN diode switch is used instead If additional phases or amplitudes are needed more MPFU are installed in parallel with the first MPFU Attenuator x Phase PIN Shifter Diode x HOr gt Hr x Shifter Diode l aa ag ails o PIN Attenuator TWT Attenuator Attenuator Phase PIN R Trans Lev HPP x x Figure 2 45 The excitation portion of the pulse bridge Two PIN diode switches are required to turn the microwaves sufficiently off so there is a second switch Pulse Gate in series with the MPFU The transmitter level attenuator controls the overall power for input to the TWT After the TWT amplifies the E 580 User s Manual 2 43 Pulse EPR Practice Detection microwave pulses the HPP High Power Pulse attenuator allows you to change the amplitude of the high power micro wave pulses In normal operation most of the attenuators and phase shifters are kept fixed except for the HPP attenuator This attenuator adjusts the B that we apply to our sample Because B is pro portional to the square root of the microwave power we need to decrease the HPP attenuator by 6 dB in order to double B4 gt gt Signal Out Vamp ees lt lt HH lt signal In Phase xJ Preamp pn Shifter Quad Power Diode Hybrid Splitter Defense gt Signal Out Vamp Figure 2 46 The detection portion of the pulse bridg
47. a hole burning experiment 2 40 akGaen Pulse EPR Practice Pulse EPR Practice Modern pulse EPR spectrometers perform an amazing feat They detect tiny lt 1 nW signals tens of nanoseconds after a powerful gt 1 kW microwave pulse and can repeat this feat every 1 us This section describes how the Bruker E 580 spec trometer accomplishes this feat 2 2 Figure 2 43 shows a photograph of an E 580 spectrometer The components are identified in the block diagram Bridge Controller Field Controller Digitizer Acquisition Server Pulse Programmer Resonator LA Power Magnet Supply Figure 2 43 A photograph and block diagram of a Bruker E 580 spectrometer E 580 User s Manual 2 41 Pulse EPR Practice Many of the components such as the magnet resonator etc should be familiar from your experience with a CW EPR spec trometer The TWT Travelling Wave Tube is a high power microwave amplifier that produces the 1 kW microwave pulses There are more components to be controlled in a pulse bridge so a second Bridge controller is required in addition to the standard MBC Microwave Bridge Control board The pulse program mer produces pulses that orchestrate all the events to produce high power microwave pulses protect receivers and trigger acquisition dev
48. and ESEEM with a PulseSPEL program We could have just as easily inter changed our measure methods but we would run into a vexing factor of two discrepancy The cause of this discrepancy is that the pulse tables use abso lute timing whereas the PulseSPEL uses timing relative to the last event First let us consider the pulse table timing When we perform the experiment in Section 5 4 the time between the two microwave pulses is d1 dx where d1 is the initial separation and dx 8ns is the step size The echo should occur at d1 dx d0 after the lead ing edge of the second pulse where d0 is an instrumental delay factor Therefore the position of the acquisition trigger should be dl dx d1 dx d0 2d14 2dx d0 D 1 Therefore the step size for the echo decay is 2dx i e 16 ns us i 2 T I l ke le gt p dit dx l d1 dx d0 J I l 2d1 2dx d0 l l l l l 0 Second Acquisition Pulse Trigger Position Position Figure D 27 Pulse table timing D 42 W J A m a i Pulse Tables vs PulseSPEL This is precisely what we want for a T measurement because the dephasing occurs between the first microwave pulse and the top of the echo What happens if we try to measure the echo decay with the Pulse SPEL program Here d1 dx is again the spacing between the two microwave pulses However in a PulseSPEL program the delay for the Acquisition trigger
49. and imaginary components of the magnetization and are com monly labeled Channel a and Channel b There is a phase shifter to adjust the reference phase for the quadrature detection This phase rotates the detection axes and therefore changes the appearance of the signal In Figure 2 49 we start with an on resonance FID and the reference phase adjusted so that we only have a signal in Channel a If we were to change the refer ence phase some of the signal in Channel a appears in Channel b and vice versa b Im 90 re N b a Pe 9 Ro a b a acos b sin b b asing b cos Im 90 a __ are A 6 i a Figure 2 49 The effect of the reference phase on the signal 2 46 i Pulse EPR Practice The quadrature detection is followed by one more stage of amplification and filtering by the VAMP Video Amplifier Both the gain and bandwidth of the VAMP are adjustable Six dB steps are required to change the signal amplitude by a factor of two The bandwidth is normally kept at the maximum value 200 MHz Narrower bandwidth reduces the noise but also dis torts higher frequency signals There are a few cases See page 2 56 and Appendix B where the bandwidth must be reduced Figure 2 50 shows the effect of bandwidth reduction on the FT EPR spectrum Note that there is both a time shift and an attenuation of higher frequency components of the spectrum at narrower bandwidth
50. at room temperature 300 K with a sample with 10 000 spins on average 5 004 spins would be par allel and 4996 spins would be anti parallel resulting in a popula tion difference of only 8 At room temperature and X band we are dealing with a small population difference between the two States When we apply a 2 2 pulse to our sample we no longer have thermal equilibrium How does this happen When B rotates the magnetization into the x y plane the magnetization along the Z axis goes to zero i e the population difference goes to zero See Figure 2 14 If we were to use Equation 2 9 to estimate the temperature of our spins we would obtain T Our spin system is obviously not in thermal equilibrium and through its interactions with the surroundings it will eventually return to thermal equilibrium This process is called spin lattice relax ation 80000 000000 806060 x M n 2 Pulse mt Pulse Equilibrium Figure 2 14 Populations before and after 7 2 and z pulses 2 16 i Pulse EPR Theory 1 M Ma Figure 2 15 We could go even one step further and apply a x pulse This will actually rotate the magnetization anti parallel to the z axis cor responding to more magnetic moments aligned along the z axis This is why a z pulse is often referred to an inversion pulse If we use Equation 2 9 we actually calculate a negative tempera ture The rate constant at which M re
51. curve to your inversion recovery E 580 User s Manual 6 17 Inversion Recovery with Echo Detection The value Tau is the fitted T value it should be approxi mately 250 ps Exponential Decay Commands Figure 6 16 Fitting an exponential to the inversion recovery 6 18 shg Inversion Recovery with Echo Detection 16 Fit a decaying bi exponential to measure T4 The inversion recovery is seldom a single exponential because of spin diffusion and other effects Click the Biexponen tial Decay command in the Exponentials submenu of the Fitting subnenu The Biexponential Decay dialog box appears Click the Fit button and the program will fit a two exponential curves to your inversion recovery prFitBiexp Slice amplitude 1 fit amplitude 1 Tau 1 fit Tau 1 amplitude 2 fit amplitude 2 Tau 2 fit Tau 2 y offset fit y offset gt current vall 682 67433 yes vino ESEE yes vno zsm yes v no pann yes vro 891 87171 A yes vro E B L 2 Fit Function y a exp x fb c exp x d e Figure 6 17 Fitting a bi exponential to the inversion recov ery E 580 User s Manual 6 19 Three Pulse ESEEM Three Pulse ESEEM 6 2 In this section we shall measure the three pulse ESEEM of the coal sample As we discussed on page 2 38 three microwave pulses produce five echoes
52. cycle Save the spectrum E 580 User s Manual Inversion Recovery with Echo Detection Find where the echo bottom is Place your cursor on the spectrum and determine from the readout at what time the bottom of the inverted echo occurs See Figure 6 9 Record this number somewhere We shall use this value for dO in the next section Figure 6 9 The inverted echo The Inversion Recovery Experiment 6 1 2 l 2 Follow the instructions of Section 6 1 1 Edit the PulseSPEL program The edited PulseSPEL program from Step 7 of Section 6 1 1 needs a bit of modification to suit our needs Make the changes indi cated in Figure 6 10 The second and fourth highlighted sections are a bit tricky The first line of the second sec tion needs the semi colon that we added at the beginning of the line deleted The fourth section needs a semi colon at the beginning of the line to comment it out W J A m a Inversion Recovery with Echo Detection i i cho detected inversion recovery echo detected inversion recover A L Ne Ne Ne Ne Ne Ne begin defs begin defs dim s 1024 1 dim s 1024 1 end defs end defs L L r r begin lists begin lists phi x asgl a bsgl b end lists r end lists r F begin exp SPT QUAD i begin exp SPT QUAD sweep x 1 to sx shot i 1 to h sweep x 1 to sx p2 ph shot i l to h d2 p2 phl dx d2 a BO tere d1 pl x dl do pl
53. disappears We have already seen that electron spins in a magnetic field are characterized by two quantum mechanical states one with the magnetic moment parallel and the other state with the magnetic moment anti parallel to the magnetic field The moments will be randomly distributed between parallel and anti parallel with slightly more in the lower energy parallel state because the elec tronic system obeys Boltzmann statistics when it is in thermal equilibrium Then the ratio of populations of the two states is equal to _AE Nanti kT anti parallel _ 2 2 9 Darallel where n represents the populations of the two states AE is the energy difference between the two states k is Boltzmann s con stant and T is the temperature The magnetization that we have been discussing so far is actu ally the vector sum of all the magnetic moments in the sample Since the moments can only be either parallel or anti parallel the magnetization is simply proportional to the difference E 580 User s Manual 2 15 Pulse EPR Theory Technically speak ing temperature is not defined in a non equilibrium condition so nega tive and infinite temperatures do not violate any ther modynamic laws s 000000 z 2 M 7 y x x Thermal Dyarallel Banti parallel Wd will be aligned along the z axis To get an idea of the size of the population differences if we are work ing at X band 9 8 GHz
54. down menu contains commands associated with com pilation tasks such as compiling validating and aborting compi lations Compile Compile Compile With Validity Check Abort Verbose Show Variable Definitions Figure D 23 The Compile drop down menu This command performs two different functions It initializes the PulseSPEL variables with the current definitions if the variable E 580 User s Manual D 39 PulseSpel Programming Panel Compile with Validity Check Abort Verbose Show Variable Definitions Properties definitions are currently displayed This initialization is required before compiling a PulseSPEL program If the PulseSPEL pro gram is displayed the program is compiled Any messages are displayed in the message display area See Figure D 9 If the PulseSPEL program is displayed the program is compiled and each individual instruction and variable value is checked for validity Validity is defined as safe and within the capabilities of the spectrometer If a program and variable definitions are found to be invalid the software will not allow you to run the experi ment It is strongly recommended to always use this command instead of the Compile command This command does not ini tialize the PulseSPEL variables Any messages are displayed in the message display area See Figure D 9 Aborts a compilation or validity check This option causes the message display area to displa
55. experiments is ESEEM Electron Spin Echo Envelope Modulation The electron spins interact with the nuclei in their vicinity and this interaction causes a peri odic oscillation in the echo height superimposed on the normal echo decay The modulation or oscillation is caused by periodic dephasing by the nuclei If we subtract the decay of the spin echo and Fourier transform the oscillations we obtain the split tings due to the nuclei Armed with this information you can identify nearby nuclei and their distances from the electron spin and shed light on the local environment of the radical or metal ion ay PM ih HN W PRAT Aten T T T 0 2000 4000 6000 8000 10000 12000 14000 16000 18000 20000 22000 24000 26000 28000 30000 32000 Figure 2 38 Modulation of the echo height with t due to ESEEM a O A 012 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 MHz Figure 2 39 The Fourier transform of the ESEEM showing proton couplings E 580 User s Manual 2 37 Pulse EPR Theory Stimulated Echoes Hahn or two pulse echoes are not the only echoes to occur If we apply three 1 2 pulses we obtain five echoes Three of the ech oes are simply two pulse echoes produced by the three pulses The stimulated and refocused echoes only occur when you have applied more than two pulses lel Stimulated imulate a i eee Echo Hahn Hahn 2 3 7 Refocused
56. experiments together in one Puls eSPEL program organizes the experiments required for a partic ular task Multiple lists function in the same way as a single list except that each additional list is labeled by lists where is a number from 1 to 15 The first lists section must still be labeled lists with no number suffix Each list can be given a name delimited by quotation marks that is displayed in the Phase Cycle drop down menu of the PulseSPEL Acquisition panel See Section D 2 Each lists statement begins with begin lists and ends with end lists Multiple experiments function in the same way as a single experiment except that each additional experiment is labeled by exp where is a number from 1 to 15 The first exp section must still be labeled exp with no number suffix Each experi ment can be given a name delimited by quotation marks that is displayed in the Experiment drop down menu of the Puls eSPEL Acquisition panel See Section D 2 Each exp state ment begins with begin exp and ends with end exp The multiple lists and exp sections work independently of each other We could for example select the second phase cycle lists1 and use it with the third experiment exp2 In contrast there must be a one to one correspondence between the dataset size declared in an individual dim statement and that required by the corresponding experiment definition Therefore dim where is a number between one and eight or blank must c
57. gt 0 Integrated Area 0 wen afr ee ee AET anal I Figure 2 55 Suppression of off resonance effects by signal integration E 580 User s Manual 2 53 Pulse EPR Practice Figure 2 56 Linewidths for different integration times with selective detection for echo detected field swept spectra 2 54 Pulse EPR Practice Transient The transient recorder is extremely efficient at recording and Recorders signal averaging FIDs and echoes because it captures a complete signal in one acquisition In this mode the SpecJet is functioning like a digital oscilloscope Acquisition 1 Figure 2 57 Capturing of a signal in one acquisition with a transient recorder E 580 User s Manual 2 55 Pulse EPR Practice Aliasing To use a digitizer effectively we need to be careful about the rate at which we sample the signals We must make sure that we ful fill the Nyquist criterion Vmax lt VN gt 2 29 where Vmax 18 the highest frequency in our signal and the Nyquist frequency is Vy 1 2At 2 30 where At is the time between the points in the digitized signals If we do not comply with this condition we get fold over or aliasing when we Fourier transform the signal See Figure 2 58 A lower frequency component equally fits the digitized points and the signal will appear as a lower frequency This foldover effect or aliasing is one of the reason
58. increase Q so we must increase the proportionality constant It is optimized for a given sample diameter in small resonators such as dielectric and split ring resonators Q 100 5000 Q 100 1000 B A B Dielectric Resonator Split Ring Resonator Figure 2 63 Two types of resonators Bruker uses for pulse EPR The high range of the Q values are for a matched resonator The low range is for an over coupled resonator E 580 User s Manual 2 61 Pulse EPR Practice In CW EPR we normally critically couple the resonator The two pulse resonators still have too high a Q when matched so we need to further decrease the Q by overcoupling the resonator This does mean some of the microwave power is reflected back thereby decreasing the power to the sample but we need to com promise and minimize the deadtime rT L off resonance vs r overcoupled r gt v critically coupled l i v ji i it l it it 400 800 1200 4600 2000 fns Figure 2 64 Tuning mode patterns and reflected power for critically coupled and overcoupled resonators Notice that no microwave power is reflected when on resonance and critically coupled 2 62 Pulse EPR Practice Phase Cycling 4 Step Phase Cycle 2 2 5 Phase cycling serves two purposes to suppress artefacts due to imbalances in the quadrature detection and to eliminate unwanted FIDs and echoes The phas
59. into the PulseSPEL Variable box and then press the Enter key If you wish to verify that the dO value has indeed changed type in dO and press the Enter key to view the new value FTEPR Parameters Pattems Field RF Acquisition l Scan l Options l ABSCISSA QUANTITIES AND SIZES X Axis Quantity Time y X Axis Size 512 Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE Run from Tables R Run from PulseSPEL Erten PulseSPEL w Read Transient Vari able wv Start Transient B Ox PulseSPEL ACQUISITION PulseSPEL Program SPEL2 fidcycle_bcstep exp PulseSPEL Variable d0 40 ns Experiment EXP y Phase Cycling LISTS y Phase Program Normal y Figure 4 14 Editing PulseSP 12 13 Close PulseSPEL Help EL variables Press the Run button The spectrometer then acquires the FID and it appears in the viewport Save the spectrum E 580 User s Manual 4 13 Processing the FID Processing the FID 4 3 The FID looks pretty but it is not the ideal representation for our data In order to obtain a frequency representation we need to Fourier transform our time domain data We shall use the FFT Fast Fourier Transform to achieve this result Prior to trans forming the data we need to perform some baseline corrections as well as some left shifts of the data After the transformation we may need
60. iustipeopleirtwixeprFiles PulseSPEL Create File show Filenames Select a program to replace or type a new path filename swe Cancel Help Figure D 14 The Save Variable Definitions As dialog box It can be rather inconvenient to continually choose the Path To set the default PulseSPEL directory click PulseSPEL Path and a dialog box appears in which you can enter the desired default Path Click Set when you have entered the new Path name Now when you load or save the Path will be the Path that you set agPgPath Path AisripeopleirtwixeprFiles PulseSPEL Enter the path and click OK Set Cancel Help Figure D 15 The PulseSPEL Path dialog box E 580 User s Manual D 35 PulseSpel Programming Panel Edit D 4 2 This drop down menu contains commands associated with edit ing tasks such as cutting and pasting Undo Bedo cut Copy Paste Select Line at Number What Line Number Show Caret Figure D 16 The Edit drop down menu Undo You may choose to undo the last editing operation or undo all the editing operations since you loaded the particular variable definition or PulseSPEL program file Undo F Redo r t Copy Paste Select Line at Number What Line Number Show Caret Figure D 17 The Undo submenu D 36 B PulseSpel Programming Panel Redo Cut Copy Paste Select Line at Number What Line Numbe
61. ives 7 1 7 1 The HYSCORE Setup Experiment c ccccscesccossssssessncssecsessncsecceeases 7 2 7 2 The HYSCORE Experiment ssseesseseesseesesseseeseessessrssrossessessresseesees 7 10 Appendix A FlexLine Resonators cccsseeeeeeeeseeeeeeeeeeees A 1 Al Resonator Description y s cice oss anena a a ER A 2 A 1 1 The Probehead Support ccccccccccscesseeceeeseesceeeseeeceseceseeesseseeeeseeeseenseenes A 4 A1 2 The Resonator Module vce reisens ioie iania i iei i EE A 7 A 1 3 The Sample Holdets 2 s beseissaecdeeschadzcass soavehliaeaatedasste0gizdeaddieiesedinsadees A 8 A 1 4 The Sample Rod ccceccccccssscessceseeeeeeseeeseecseceseceseceeeeeseeeseeceeeeeseeseeennes A 10 A 1 5 The Waveguide SMA Transition cccccccesseeseestecsteceeeseeeeeteeeseeeseeaees A 11 A 1 6 The Semi rigid Coaxial Cable cccccccccesceesseesseetecenseenecseeeseeeeeeeneeenaes A 11 Aile T TOONS oui szateseanstcseeconbectieay tense steonea ss tesasfens cea catauanves dh conse E E EE A 11 A 2 Installing ne Resonator ssccd ccc to vas tars ecsdaksuinbenulia da deka neds Seeuee A 12 A 3 Variable Temperature Operations inetd kG ces Seccasts ed Seine shelueentss A 15 E 580 User s Manual ix Table of Contents A 3 1 Temperature Rangen a r a aaa aa al EAA ENEE aaa A 15 A 3 2 Changing Samples Using the ER 4118CF Cryostat seseseseseessesesseees A 15 A 3 3 Gas Flow for Room Temperature Operation cccccces
62. of Section 7 1 d30 16 ns d31 16 ns pO 16 ns p2 Determined in Step 13 of Section 7 1 h 5 Table 7 2 Variable values for the HYSCORE experiment Press the Run button The spectrometer will acquire the stimulated echo decay This acquisition will take a while because it is a two dimensional experiment Save the spectrum Phase the data The real data should be a slowly decay ing exponential and the imaginary data should be flat If you followed the directions in Section 4 1 correctly phasing should not be necessary If there is an appreciable amount of signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat E 580 User s Manual 7 13 The HYSCORE Experiment 11 Extract the real part of the dataset Once properly phased only the real part of the dataset contains the infor mation we seek Click the Real Part command of the Complex submenu of the Processing menu Processing Diff amp Integ Filtering Algebra Peak Analysis Complex Window Functions Absolute Transformations Power bragiiy Fitting Structure XSophe ProDeL Automatic Real Part Imag Part Re lt gt Im Conjugate Figure 7 14 The Real Part command Real Part Command 12 Click the Baseline Correction task button fol lowed by the Polynomial task button The polyno mial baseline correction task bar then a
63. of the microwave pulses and the starting time for the data acquisition The software does all the rest of the work for us E 580 User s Manual 2 49 Pulse EPR Practice Data Acquisition 2 2 3 Once we obtain a signal from the detection portion of the bridge we need to digitize it somehow to process the signal with a com puter There are three different classes of digitizer required for pulse EPR spectroscopy point digitizer integrator and transient recorder See Figure 2 52 The SpecJet digitizer performs these three classes of experiments as well as signal averaging to improve the signal to noise ratio of the signal Point Digitizer Samples one point at a time requiring multiple acquisitions ESEEM amp relaxation measurements Non selective detection Integrator ESEEM relaxation measurements amp field sweeps Selective detection Transient Recorder Captures a complete waveform in one acquisition FIDs echoes FT EPR amp field sweeps Non selective detection 2 t t Fa _ Integrates signal to obtain area Sa t Figure 2 52 The three classes of acquisition devices used in pulse EPR 2 50 i Pulse EPR Practice Point Digitizers In the point digitizer mode of the SpecJet the digitizer only samples one point lt 2 ns in the FID or echo at a time thereby requiring multiple acquisitions for measuring signals See Figure 2 53 The most common measurements
64. pulse is applied to invert the longitudinal magnetization and a m 2 is applied at different times after the inversion pulse to detect the recovering magnetization We shall perform three types of echo experiments field swept echo detected EPR T phase memory time measurements from an echo decay and two pulse ESEEM Electron Spin Echo Envelope Modulation Both pulse tables and PulseSPEL pro grams will be used E 580 User s Manual Inversion Recovery with FID Detection Inversion Recovery with FID Detection 5 1 In this experiment we measure the T spin lattice relaxation time of the DPPH sample by inversion recovery The T value is approximately 100 ns which is about the lower limit for what can be measured in such an experiment A m pulse inversion pulse inverts the magnetization and we detect the height of the FID as we increase the separation between the two pulses Inversion Detection Pulse Pulse NIA Acquisition Trigger Figure 5 1 The inversion recovery experiment 1 Follow the directions in Section 4 1 up to and including Step 6 Most of the steps required to per form this experiment are already described in the previous chapter 2 Click the Stop button The PatternJet pulse program mer stops See Figure 5 2 Inversion Recovery with FID Detection 3 Program a 32 ns x pulse at 0 ns and a 16 ns pulse at 40 ns The 32 ns pulse is our x or inversion pulse and the 1
65. requiring this mode are ESEEM and relaxation measurements experiments where only the height of the echo needs to be measured For example in a two pulse experiment we generate the signal by measuring the echo height for the initial t value then step out t digitize the second point of our signal and so on until we have acquired the entire echo decay 3 eee Etc re T Acquisition 2 ie Acquisition 3 Tt gt 1 Acquisition 1 JI Figure 2 53 Acquisition of an echo decay with a point digi tizer E 580 User s Manual 2 51 Pulse EPR Practice Integrators g Soft pulses often called selective pulses are lower By and power pulses and therefore are longer pulses Hard pulses often called non selective pulses are higher B4 and power pulse and therefore are shorter pulses The point digitizer method is often called non selective detec tion whereas the integration method is called selective detec tion We shall see why this is so Because of the limited excitation bandwidth in pulse EPR we cannot always Fourier transform an FID or echo to obtain a broad EPR spectrum See Figure 2 13 We could however measure the echo height as we sweep the magnetic field to gen erate a broad EPR spectrum There is only one slight problem which is called power broadening This effect is different from power broadening in CW EPR We can easil
66. rotating frame 2 3 to 2 14 Run from Tables modes 4 4 S safety chemical 1 iv to 1 vi electrical 1 iv microwave 1 vi test 3 9 to 3 19 sample access A 6 coal 5 1 DPPH 4 1 to 4 3 5 1 position 4 3 A 9 shots per point C 2 signal averaging 2 59 to 2 60 phase adjusting 4 4 5 12 soft pulse 2 40 SpecJet Also see data acquisition averaging C 19 averages done C 19 no of averages C 19 display C 18 to C 22 time base C 19 No of Points C 19 spectral diffusion 2 36 spectrometer configuration E 1 to E 7 configuration and timing E 3 to E 5 data set selection E 4 data set E 4 delete E 4 load E 4 save E 4 pulse programmer setup E 5 channel E 5 connector E 5 delay E 5 length E 5 PDCH board E 5 time raster E 5 twt andrf E 4 RF duty cycle E 4 TWT duty cycle E 4 TWT maximum gate time E 4 TWT minimum gate time E 4 TWT recovery time E 4 options E 6 to E 7 field modulation off E 7 single point recorder type E 6 spin echo 2 34 to 2 40 splittings 2 31 SRT 2 18 C 2 STAB button 3 3 E 580 User s Manual Index stabilizer external 3 4 to 3 6 Start Transient mode 4 4 5 14 stimulated echo 2 38 6 20 to 6 29 sweep width C 8 T T 6 2 T 2 21 2 36 Ts 2 20 thermocouple A 5 tip angle 2 8 Ty 2 36 measurement acquisition 5 21 to 5 23 5 21 to 5 24 processing 5 23 to 5 24 tuning mode pattern 2 62 3 5 to 3 6 up 3 3 to 3 8 turning spectrometer off 3 23 to 3 24 on 3 2 to 3 3 t
67. the acquired waveform This avoids many of the problems that analog integrators pose such as drifts and offsets Digital integration can present a few problems if the parameters are not set up correctly Foldover caused by an excessively long time base can create artefacts and large numbers of digitized points can slow down the acquisition The following sections will assist you in properly setting param eters to avoid these effects E 580 User s Manual Timebase and Bandwidth Timebase and Bandwidth B 1 The microwave pulsewidth and the resonator bandwidth also affect the fre Because the E 580 digitizes the waveform we must take care that the time base i e the time resolution is sufficiently fine to capture all the high frequency components Or in other words we must satisfy the Nyquist criterion If we don t fulfill this cri terion the high frequency components are folded over to a lower frequency Alas these low frequency artefacts will not cancel out properly See Figure B 1 Follow this section s guidelines to avoid these problems If you are using short microwave pulse lengths in a low Q reso quency bandwidth of the signal nator only the VAMP Video AMPlifier bandwidth controls the frequency components seen in the signal The following table lists the maximum bandwidths required for different time bases You should set the VAMP bandwidth less than or equal to the approp
68. the readout at what time the top of the echo occurs See Figure 5 16 Record this number somewhere Determine the width of the echo and record it somewhere The Acquisition Trig ger should start at Acquisition Trigger echo top echowidth 2 5 1 E 580 User s Manual Echo Detected Field Swept EPR Top of Echo f AA Width of Echo _ Figure 5 16 The width and top of the echo 3 Set the Acquisition Trigger Position Enter the value determined in Step 2 into the Position box 4 Set the Acquisition Trigger Length Enter the echo width in the Length box We want the position and length of the Acquisition Trigger adjusted so that it covers most of our echo Figure 5 17 Length amp Position of the Acquisition Trigger 5 16 shg Echo Detected Field Swept EPR We are using the integrator here to narrow the detection bandwidth and there fore obtain a well resolved spectrum See Figure 2 55 and Figure 2 56 5 Set the Integrator Time Base to 4 ns FT EPR Parameters Patterns l PULSE PATTERNS RF aedis Time Base Shots per Point Channel Selection mee Trigger Integrator Time Base ns single Poit Point Single Point 4 0 Position ns Length ns Pos Disp ns Length Inc ns ae 999 6 t Shots Per Point 1 x Figure 5 18 Setting the Integrator Time Base
69. the resonator the sample rod is fully inserted through the sample access of the probehead support GE SSSSSSSSSSSSSSSSSSSSSS ht Xy Stopper Figure A 9 Attaching the sample holder onto the sample rod lt Figure A 10 Inserting the sample in the resonator Resonator Description The Waveguide SMA Transition A 1 5 The FlexLine Series resonators use semi rigid coaxial cable instead of conventional waveguide The waveguide SMaA transi tion adapts the waveguide bridge output to the semi rigid coaxial cable Also included with the resonator are the required waveguide gasket and waveguide screws for attaching the transi tion to the bridge The Semi rigid Coaxial Cable A 1 6 Tools 8 mm Wrench 1 4 inch Wrench 2 5 mm Allen Wrench The semi rigid coaxial cable connects the bridge and the resona tor It has male SMA connectors on both ends of the cable As the name implies it is bendable however it is advisable to be gentle if you need to bend it for proper fit Do not make very sharp bends as it may cause the cable to kink A 1 7 Included with the resonator are three tools for exchanging the resonator modules and attaching the semi rigid cables This wrench is used to tighten the male SMA connectors This wrench is used to prevent rotation of the cable while the male SMA connector is tightened with the 8 mm wrench The 2 5 mm Allen wrench is used to loosen and tighten the screws that fasten the r
70. the wing nut E 580 User s Manual A 13 Installing the Resonator The SMA connector must be tight i e you need a wrench to loosen the connec tions but do not overtighten the SMA connectors Over tightening will either cause reflections or worse yet break the SMA connector Use of an SMA torque wrench ensures proper tightening Follow the instruc tions in reverse order if you wish to remove the resona tor Attach the semi rigid cable to the microwave connector on top of the resonator assembly Only fasten it finger tight so that the cable can still be rotated Attach the other end of the semi rigid cable to the waveguide SMA transition You may need to rotate or gently bend the cable for everything to fit Firmly yet gently tighten the connector on the cable with the sup plied 8 mm wrench Semi rigid Cable Figure A 14 Connecting the resonator assembly and the bridge Firmly yet gently tighten the connection between the semi rigid cable and the resonator assembly Use the 8 mm wrench to tighten the male SMA connector while using the 1 4 inch wrench to prevent the female SMA connector from rotating Connect the modulation cable to the modulation connector A 14 Variable Temperature Operation Variable Temperature Operation A 3 Temperature Range A 3 1 The FlexLine resonators may be used safely from 4 2 to 350 K with the ER
71. to connect the modulation wires They also have cable restraints to keep the modulation and thermocouple wires in place The designation for a module is ER 4118 Band Module Diameter Window Band Module Diameter Window X MD Dielectric 3 3mm Sample None Resonator Access S MS Split ring 5 5mm Sample W1 1 Window Resonator Access L W2 2 Windows Table A 2 Possible values for the resonator module designation E E j Restraint Modulation Aesan Pins LE ON Optional Optical Window Figure A 5 Front and back views of an ER 4118 xxx resonator module E 580 User s Manual A 7 Resonator Description The Sample Holders A 1 3 There are five different sample holder sizes with 1 2 3 4 and 5 mm diameter holes Choose the smallest sample holder that A allows your sample tube to be comfortably inserted into the holder The sample is inserted through the threaded end See Figure A 6 The sample rods will not allow the use of iai plastic caps on the il sample tubes Figure A 6 Proper way of inserting a sample tube into the sample holder Spring fingers inside the sample holder gently grip the sample and but still allow the sample to be pushed with your fingers If the sample slips out of the sample holder under its own weight the sample holder needs to be tightened Remove the sample insert a screwdriver in the slot and gently turn the di
72. to trans form our time domain data to the frequency domain 1 Select the FFT command Click its button in the Transformations submenu of the Processing menu Processing Diff amp Integ F Filtering Algebra r Peak Analysis ca Complex td Window Functions FFT Command Transformations F smaga Zero Filling Fitting _ FFT Structure FFT Real prFFTopix XSophe 2D FFT ProDeL _ Gross Term Averaging Slice v current all Automatic Epnvolution Type fwd vin undo Derenvekstion i gt 2 Symmetrization Transform Cancel Help Invert Abscissa g Factor SORT of Abscissa Transform lores serra Button _ Normalize Integrals Eaa n Left Right Shift Polar to Rect Rect to Polar Linear Figure 4 24 The FFT command 2 Click the Transform button The default options are appropriate for what we are doing The result will appear in the Primary dataset The results of the FFTs is pre sented in the figures on the next few pages 4 20 ekGaen Processing the FID 0 049999 Figure 4 25 FFT of the Section 4 1 1 dataset after baseline correction and left shift Figure 4 26 FFT of the Section 4 1 2 dataset after baseline correction No left shift is required Notice that it is the same as Figure 4 25 E 580 User s Manual 4 21 Processing the FID Artefact a 0 049999 Figure 4 27 FFT of the Section 4 1 3 dataset after baseline correction No
73. to verify that it is within the limits of the spectrometer capabilities If successful the statement Second pass ended appears in the message window PulseSPEL Programming Panel hyscore_set exp dir usripeopleirtwixeprFilesiPulseSPELisharedPt File Edit Search Compile Properties Options HYSCORE setup program with 4 element phase rotation Load Var Def Save Program Save Var Def begin defs dim s 256 1 Show Program end defs Show Var Def begin lists SSeS phl x x x x coe ph2 x x x x asgl a a a a C Psgl b b b b end lists begin exp SPT QUAD dx 0 dy 0 sweep x 1 to sx shot i 1 toh po x d1 po x d2 E Message Window 7 Help On Selection Pa Loaded file usr people rtw xeprFiles Pulse SPEL shared Pulse SPEL Standard PulseSPEL2000 SPEL2hy Validating the PulseSPEL program 9 Close the PulseSPEL window Double click the close button 7 6 ioe BROKER CoO The HYSCORE Setup Experiment po po p2 po Acquisition Z Z Z Trigger d1 t d2 d3 t d1 ia dx Figure 7 8 Variable definitions for the modified hyscore_set exp 10 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 7 8 Set the variables to the values indi cated in Table 7 1 Variable Value d1 128 ns d2 200 ns d3 200 ns do 0 ns d30 4 ns po 16 ns
74. until the echo is not clipped but the echo still fills a sub stantial portion of the SpecJet display E 580 User s Manual 5 11 A Standing Hahn Echo Adjust the magnetic field to bring the sample on resonance Depending on the Signal Phase we will see the signal in both quadrature channels See Figure 5 12 Use the Field Position and not the Center Field to adjust the field This gives you faster and more precise control of the field 10 000 5 000 5 000 10 000 10 000 5 000 0 500 1 000 5 000 10 000 1500 2000 0 500 1 000 1500 2 000 Time ns 0 Time ns Figure 5 12 Almost on resonance coal echo Left display is not properly phased Right display is properly phased 11 Adjust the phase Use the Signal Phase slider bar in the microwave bridge menu to adjust the phase until most of the echo is in the real channel See Figure 5 12 The small amount of first derivative echo in the imaginary channel indicates we are not exactly on resonance A Standing Hahn Echo Notice the FIDs after each microwave pulse in Figure 5 13 The coal linewidth is still narrow enough that the FID extends past the deadtime of the spectrometer 12 Fine adjust the parameters Repeat Steps 10 and 11 until the traces look those in Figure 5 13 10 000 10 000 0 500 1 000 1500 2000 0 Time ns Figure 5
75. 1 The magnetization of your sample can often undergo very com plicated motions A useful technique widely used in both CW and FT EPR and NMR is to go to a rotating coordinate system referred to as the rotating frame From this alternative point of view much of the mathematics is simplified and an intuitive understanding of the complicated motions can be gained A simple analogy for the rotating frame involves a carousel and two people trying to have a conversation One person is riding on the carousel and the other person is standing still on the ground Because the carousel is moving the two people will be able to speak to each other only once per revolution and no meaningful conversation is possible If however the person on the ground walks at the same speed as the carousel is rotating the two people are next to each other continuously and they can carry on a meaningful conversation because they are stationary in the rotating frame The presentation is based on classical mechanics the classical picture is often clearer and more productive than the quantum mechanical picture Even though the phenomenon on a micro scopic level is best described by quantum mechanics we are E 580 User s Manual Pulse EPR Theory Magnetization in the Lab Frame measuring a bulk property of the sample namely the magnetiza tion which is nicely described from a classical point of view In order to describe a physical phenomenon we n
76. 13 Properly phased on resonance echo from a coal sample exhibiting FIDs 13 Adjust the HPP attenuator to maximize the echo This value is typically about 5 dB See Figure 3 10 E 580 User s Manual A Standing Hahn Echo 14 Select Start Transient Click the Start Transient but ton in the Acquisition panel faeere Figure 5 14 The Acquisition panel 15 Press the Run button See Figure 5 5 The spec trometer then acquires the echo and it appears in the view port 16 Save the spectrum 5 14 BRORER Echo Detected Field Swept EPR Echo Detected Field Swept EPR 5 3 In this experiment we shall acquire a field swept echo detected EPR spectrum of our the coal sample using the pulse tables Field swept experiments are used to acquire broad EPR spectra in which we cannot excite the whole spectrum for an FT spec trum From the spectrum we can then choose field positions to perform further experiments We shall perform a standing echo experiment in which we integrate the area under the echo while we sweep the magnetic field The integration limits the detection bandwidth thus yielding a better resolved spectrum compared to just measuring the echo height See Section 2 2 3 400 ns Integrator Gate Figure 5 15 The echo detected field swept experiment 1 Follow the instructions of Section 5 2 2 Find where echo begins and ends Place your cur sor on the spectrum and determine from
77. 2 acquisition 7 10 to 7 13 processing 7 13 to 7 22 setup 7 2 to 7 9 inhomogeneous broadening 2 19 integration 2 53 to 2 54 B 1 to B 4 bandwidth B 2 to B 3 E 580 User s Manual Index foldover B 2 integrator timebase B 2 to B 3 SRT and number of points B 4 integrator See data acquisition integrator time base 5 17 introduction 1 1 to 1 3 inversion recovery echo detected 6 2 to 6 19 acquisition 6 10 to 6 15 processing 6 16 to 6 19 setup 6 3 to 6 9 FID detected 5 2 to 5 8 acquisition 5 2 to 5 6 processing 5 6 to 5 8 L laboratory frame 2 4 to 2 5 Larmor frequency 2 4 to 2 5 left right shift 4 18 to 4 19 linewidth 2 31 lorentzian 2 19 2 21 2 24 to 2 25 2 29 to 2 30 magnetic field adjustment 5 12 magnitude spectrum 4 26 to 4 27 HYSCORE 7 20 three pulse ESEEM 6 39 two pulse ESEEM 5 43 microwave circularly polarized 2 6 connections A 6 linearly polarized 2 6 magnetic field See B4 phase 2 9 power adjustment 6 28 optimizing 4 4 5 13 modulation A 5 MPFU 2 43 N normalize axes HYSCORE 7 20 three pulse ESEEM 6 39 two pulse ESEEM 5 43 number of points C 7 Nyquist criterion 2 56 O off resonance effects 2 11 to 2 14 offset 3 16 o ring A 6 A 10 A 12 overcoupling 2 62 3 6 Index P PatternJet See pulse programmer phase amp amplitude adjustment F 1 to F 13 coarse adjustment F 2 to F 9 fine adjustment F 10 to F 13 setup F 1 to F 2 angle 2
78. 2 18 2 22 i Pulse EPR Theory The transverse magnetization can then be represented by a vec tor in the x y plane It has both a magnitude M and a direction represented by the phase angle 9 Im Re Figure 2 20 Representation of the transverse magnetization as a complex quantity The reason why we go to this representation is because we can now use Fourier theory Fourier theory relates a time domain signal with its frequency domain representation via the Fourier transform This transform is the means by which we extract our EPR spectrum from the FID It is not the purpose of this primer to make you an expert in the arcane secrets of Fourier theory A few theorems and identities can offer you an intuitive and visual understanding of many things you will encounter in pulse EPR E 580 User s Manual 2 23 Pulse EPR Theory The Fourier We can represent a function either in the time domain or the fre Transform quency domain It is the Fourier transform which converts between the two representations The Fourier transform is defined by the expression i iot F fie dt 2 19 We shall use lower 0 case letters to denote the time domain rep resentation f t and There is also an inverse Fourier transform upper case letters to denote the fre t quency domain rep 1 iat resentation F f t on F e do 2 20 T 0 Fourier Transform We do not neces
79. 23 correction 4 23 to 4 26 echo decay 5 23 field swept echo detected EPR 5 20 5 34 HYSCORE 7 13 inversion recovery echo detected 6 16 FID detected 5 6 three pulse ESEEM 6 33 two pulse ESEEM 5 38 cycle echo detected inversion recovery 6 2 four step for FID 4 8 HYSCORE 7 1 three pulse ESEEM 6 20 cycling 2 63 to 2 66 memory time See Ty optimizing 5 12 program continuous D 22 next cycle D 22 normal D 22 skip program D 22 phasing 2 46 pulse EPR bridge 2 42 to 2 47 length and bandwidth 2 39 to 2 40 patterns panel C 16 to C 17 programmer 2 48 to 2 49 pulsed EPR practice 2 41 to 2 66 theory 2 1 to 2 40 PulseSPEL acquisition panel D 21 to D 22 experiment D 21 phase cycle D 22 phase program D 22 PulseSPEL program D 21 PulseSPEL variable D 22 commands and operations D 8 to D 13 for next loops D 11 acq D 9 algebraic operations D 9 to D 10 bestep D 13 bsweep loops D 12 d0 d31 D 8 dig D 9 p0 p31 D 8 rfsweep loops D 13 scansdone D 13 shot loops D 10 sleep D 13 sweep loops D 10 totscans D 13 compile D 24 multisection programs D 16 to D 20 defs D 16 exp D 16 lists D 16 programming panel D 29 to D 41 compile D 39 to D 40 abort D 40 compile D 39 compile with validity check D 40 E 580 User s Manual Index show variable definitions D 40 verbose D 40 edit D 36 to D 38 copy D 37 cut D 37 paste D 37 redo D 37 select line at number D 37 show caret D 38 undo D 36 what line number D 37
80. 4118CF cryostat With the ER 4118CV ER 4118CV M and ER 4118CV MO cryostat the range is 100 K to 323 K Under no circum stances should the resonator be sub jected to tempera tures greater than 50 C Permanent damage may result Changing Samples Using the ER 4118CF Cryostat A 3 2 The ER 4118CF cryostat operates under negative pressure tg therefore precautions are required to avoid leaking air into the E cryostat during low temperature operation Air quickly forms air ice upon contact with the cold cryostat and resonator resulting in blockages and stuck coupling mechanisms Following these To prevent air leaks instructions ensures safe and easy sample exchange arp ea pa 1 Wear safety glasses Samples that have not been o ring in the sample properly sealed may explode when they warm up BOERS e 2 Prepare your next sample Have the sample mounted as the o ring around thewampla rod stop in the sample holder sample rod assembly See per for wear or dam Section A 1 3 and Section A 1 4 age Replace them if 3 damaged or worn Turn the diaphragm pump off Make sure that the needle valve on the flow controller is not closed E 580 User s Manual A 15 Variable Temperature Operation You don t have to frantically rush to insert the next sam ple but it is advis able to insert the next sample ina timely fashion after the previous sample has been removed If you are de
81. 6 ns pulse is our 7 2 or detection pulse Start amp Stop Buttons Figure 5 2 Programming the inversion and detection pulses 4 Click the Start button The PatternJet pulse program mer starts again See Figure 5 2 E 580 User s Manual 5 3 Inversion Recovery with FID Detection 5 Adjust the Acquisition Trigger position Adjust until the inverted FID is at the left edge of the SpecJet dis play 10 000 5 000 5 000 10 000 0 500 1000 1500 2 000 0 Time ns Figure 5 3 Inverted FID with the Acquisition Trigger properly adjusted 6 Program the position displacement Set the posi tion displacement Pos Disp to 8 ns for the 16 ns x pulse and the Acquisition Trigger 7 Set the Shoots Per Loop This value specifies the number of times the signal is averaged Set it to 50 See Figure 5 2 Inversion Recovery with FID Detection 8 Select Run from Tables Verify that the Run from Tables option is selected in the Acquisition panel X Axis Quantity Window Time Magnetic Field Run from Tables Button EXP LISTS Figure 5 4 The Acquisition panel X Axis Size Window 512 Normal 9 Set the X Axis Size Set the value to 512 See Figure 5 4 10 Set the X Axis Quantity Select the Time option See Figure 5 4 E 580 User s Manual Inversion Recovery with FID Detection 11 Press the Run button T
82. 71 3 Getting Started vies ccrsiectesacerciddn naa e aE er E e LAIA EE 3 1 3 1 Turning the Spectrometer On sssssssessessesseessessrserssressessrssressessessresseese 3 2 3 2 Tuine UD acess dire e a a Oa cones chaos a a a 3 3 Bio Safety TEST ae eo na naO EERE eae N E E EE 3 9 Dae Changing Samples erene detin a ai E E R eh 3 20 3 5 Turning the Spectrometer Off nsssssssesseessesseesesessresseesesseesseeseeserssee 3 23 4 One Pulse Experiments eesssssssesesssreeeeeerrrerrrrrrrrrreerer reee 4 1 4 1 Acquiring a FID with the Pulse Tables ee eccecceceeceeeeeereeeeeenteenees 4 2 4 1 1 The Basic Experiment 0 ccccceccccessecssecseceseceeeeeeeceeeeeseecsseeseceeaecneeeeeeeeaeesees 4 2 4 1 2 An Alternative Experiment cccccccesceeseceeeeseeesecssecnscensecnseeeseeseeeaeeesaes 4 6 4 1 3 An Additional Experiment 00 cccccccccccscesscesseceeeeeeeeseeeseeeeceeeeeseeseeeeeneentees 4 7 4 2 Acquiring a FID with Puls SPEL acess caeneiisiasauiaianasiie ties 4 8 4 3 Processing the PD os scassys aues ees rae idyaeayslacaaee adhere tent aaa nee esas 4 14 43 1 Baseline Correction ninenin calgaasoenssgh EA E dea ae ete 4 14 A322 Lett Ra ght Shift ie einser e seeds eb ae be nae i 4 18 Z We Pe ae oo Wace pee ieee eee ree rere E A ents ieee cern pe eere rere entree 4 20 4 3 4 Phasing the Spectrum scean enea estes e a anae ea Taea NE 4 23 43 5 Magnitude Specta ressone o a a TO EEEE iiaiai 4 26 5 Two Pulse Experiments areave
83. ATORY AS A HAZARDOUS ENVIRONMENT IN WHICH YOU MUST CONTINUALLY MAINTAIN A HIGH STANDARD OF VIGILANCE Do not assume a cavalier attitude the substances with which you work present very real and very serious threats to your health and safety Adhere to all currently recommended guidelines for standard laboratory safety as promulgated by governmental codes and contemporary laboratory practice Inform yourself about the specific risks that are present when you handle actual or poten tial carcinogens cancer causing agents explosive materials strong acids or any liquids that are sealed in glass containers BROKER LS Chemical Safety Specifically Be extremely careful when you handle sealed glass samples that are rapidly heated or cooled The rapid cooling of some samples may result in the formation of a solid bolus in the sample tube that may make the tube prone to explosive rup ture Educate yourself about the temperature at which chemicals evaporate When a sample gets close to the temperature at which it evaporates it may quickly become volatile In general the safety threat posed by flying glass and vio lently escaping gases and liquids should not be underesti mated Wear safety glasses face masks and other protective cloth ing whenever there is any risk of spillage breakage or explo sion Protective shields should also be employed when there is any risk of explosion Be sure that both storage and worki
84. Contents Table of Contents 0 Preface gicasteaercuu cee cui ioenesesees 0 1 Electrical Satety ss tatuiitadsaitataiociaennan 0 2 Chemical Satetyeieteas se Sets Sao ana t 0 3 Microwave Safety vnccsiaseczssseturceatseziecasdcectnseoazranss 0 4 Table of Contents s nsssesssessessesseesseeseeseesseesese 1 ntr ductonN menenie e e aes 1 1 Using this Mantial fobs taicccsstentodssuateadeataieas 1 1 1 How to Find Things cccccceescesteceteeeeeeteeees 1 1 2 Typographical Conventions s ssssseseseeeeeeeee 1153 Sp cial note Sna n a i 2 Pulsed EPR Primer cecceeeeeeee ee 2 1 Pulse EPR TRG Ory ss ccccsosiei teach eacaviseeh calaeets 2 1 1 The Rotating Frame cc ceeceeseeeseeeteeteeseees 2 1 2 Relaxation Times c ccc ccceececseeeeesssssescceeeeees 2 1 3 A Few Fourier Facts 2 1 4 Field Sweeps vs Frequency Spectra 2 1 5 Multiple Pulses Echoes ceccesseesseeteeeees 22 Pulse EPR Practice aninda 2 2 1 The Pulse EPR Bridge ececeesseesseeteeeteees 2 2 2 The Pulse Programmer cccccceceeseeeseeseeees 2 2 3 Data ACQUISILION ccccccesseceteceseeeseeeseeteeeneees 2 2 As RESONAOLS eiieeii E AS 2 2 5 Phase Cy Cling sers sectecsuesssevecasvecved vous ane 2 3 Bibliography ensien a 23 NMR oreinaren e ha E 580 User s Manual vii Table of Contents DAD E A PATEA A A AAA dew add stiaed E 2 68 233 Pulsed PN O R e r e a r a a a on r E oeae ar aT Oaeh 2
85. D 3 1 Activate PulseSPEL Click the Run from PulseSPEL button in the Acquisition panel FT EPR Parameters Patterns Field RF Acquisition l Scan l Options l ABSCISSA QUANTITIES AND SIZES X Axis Quantity Time y X Axis Size 1024 Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables 7 4 Run from PulseSPEL Quadrature Detection E aa aa Run from PulsesPEL Pod PulseSPEL even Button a ees PulseSPEL MN ek y Button y Cose PulseSPEL Help Figure D 3 The Run from PulseSPEL button 2 Launch the PulseSPEL window Click the Puls eSPEL button and the PulseSPEL appears See Figure D 4 E 580 User s Manual D 23 Setting up a PulseSPEL Experiment Load the PulseSPEL variable definitions Click the Load Var Def button and a dialog box will appear ask ing for the file and directory You need to navigate to sharedPulseSPEL Standard PulseSPEL2000 SPEL2 Select the file descr def and click the Load but ton PulseSPEL Programming Panel lt No Name gt dir Load Var eee Def Button ue Show Var Def Verbose oniort Compile Validate Compile Button Help On Selection Fle Edit Search Compile Properties Options agPgdefload isd CE of this EE a PulseSPEL Program Path aredPulseSPEL Standard PulseSPEL2000
86. ELEXSYS E 580 Pulse EPR Spectrometer User s Manual ELEXSYS E 580 PULSE EPR SPECTROMETER USER S MANUAL Author Dr Ralph T Weber Illustrators Dr Ralph T Weber Aaron H Heiss EPR Division Bruker BioSpin Corporation Billerica MA USA Manual Version 1 0 Software Version 2 1 Part Number 8637070 July 2001 ELEXSYS E 580 Pulse EPR Spectrometer User s Manual Manual Version 1 0 Software Version 2 1 Copyright 2001 Bruker BioSpin Corporation The text figures and programs have been worked out with the utmost care However we cannot accept either legal responsibility or any liability for any incorrect statements which may remain and their consequences The following publication is protected by copyright All rights reserved No part of this publication may be reproduced in any form by photocopy microfilm or other proce dures or transmitted in a usable language for machines in particular data processing systems with out our written authorization The rights of reproduction through lectures radio and television are also reserved The software and hardware descriptions referred in this manual are in many cases registered trademarks and as such are subject to legal requirements This manual is part of the original documentation for the Bruker ELEXSYS E 580 spectrometer Preface e mail FAX Tel mailing address 0 Bruker strives to supply you with instructional and accurate doc umentation
87. H fer H K ss and A Grupp Europhys Lett 6 463 1988 ESR Detected Nuclear Transient Nutations C Gemperle A Schweiger and R R Ernst Chem Phys Lett 145 1 1988 Hyperfine Selective ENDOR C B hlmann A Schweiger and R R Ernst Chem Phys Lett 154 285 1989 Optimized Polarization Transfer in Pulsed ENDOR Experiments C Gemperle O W Sorensen and R R Ernst J Mag Res 87 502 1990 Pulsed Electron Nuclear Electron Triple Resonance Spectros copy H Thomann and M Bernardo Chem Phys Lett 169 5 1990 2 72 i Bibliography Stimulated Echo Time Domain Electron Nuclear Double Reso nance H Cho J Chem Phys 94 2482 1991 A Simple Method for Hyperfine Selective Heteronuclear Pulsed ENDOR via Proton Suppression P E Doan C Fan C E Davoust and B M Hoffman J Magn Res 95 196 1991 Pulsed Electron Nuclear Double Resonance Methodology C Gemperle and A Schweiger Chem Rev 91 1481 1991 Quantitative Studies of Davies Pulsed ENDOR C Fan P E Doan C E Davoust and B Hoffman J Magn Res 98 62 1992 Fourier transformed Hyperfine Spectroscopy Th Wacker and A Schweiger Chem Phys Lett 191 136 1992 Multiple Quantum Pulsed ENDOR Spectroscopy by Time Pro portional Phase Increment Detection P H fer Appl Magn Res 11 375 389 1996 E 580 User s Manual 2 73 Notes 2 74 sD BROKER EPL Getting Started 3 This chapter descr
88. ISSA QUANTITIES AND SIZES X Axis Quantity Time y X Axis Size 1024 m Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables 4 Run from PulseSPEL Quadrature Detection E v Transient v 5 g Pulse SPEL ACQU Run from PuisesPeL Pod PulseSPEL ee Button a eS PulseSPEL Paii til y Button y Close PulseSPEL Help Figure 4 8 The Run from PulseSPEL button C gt i Acquiring a FID with PulseSPEL Launch the PulseSPEL window Click the Puls eSPEL button and the PulseSPEL appears See Figure 4 9 Load the PulseSPEL variable definitions Click the Load Var Def button and a dialog box will appear ask ing for the file and directory You need to navigate to sharedPulseSPEL Standard PulseSPEL2000 SPEL2 Select the file descr def and click the Load but ton PulseSPEL Programming Panel lt No Name gt dir Load Var Def Button Compile on Button Help On Selection File Edit Search Compile Properties Options He agPgdefload siz Contents of this ae E Pulse SPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File sar def show Filenames Load Cancel Help Load Button Figure 4 9 The PulseSPEL window E 580 User s Manual Acquiring a FID with PulseSPEL 5 Compile the variable definitions Click the Compile button See Figure 4 9 This
89. In order to suppress the unwanted echoes we shall use a PulseSPEL program using the phase cycle shown in Figure 6 18 A X X X B X X X X X X A B C D D X X X Figure 6 18 A phase cycle to eliminate unwanted echoes in a stimulated echo experiment 6 20 W J A m a i Three Pulse ESEEM Setup Experiment 6 2 1 1 Follow the instructions of Section 5 2 Follow the steps up to and including Step 13 2 Activate PulseSPEL Click the Run from PulseSPEL button in the Acquisition panel Figure 6 19 The Run from PulseSPEL button E 580 User s Manual 6 21 Three Pulse ESEEM Load Var Def Button Compile Button Launch the PulseSPEL window Click the Puls eSPEL button and the PulseSPEL window appears See Figure 6 20 Load the PulseSPEL variable definitions Click the Load Var Def button and a dialog box will appear ask ing for the file and directory You need to navigate to sharedPulseSPEL Standard PulseSPEL2000 SPEL2 Select the file descr def and click the Load but ton PulseSPEL Programming Panel lt No Name gt dir File Edit Search Compile Properties Options He Help On Selection _agPgDefload Ci F Pulse SPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File sar def 1 show Filenames Load Cancel Help Contents of this i a A Load Button
90. L Acquisition Panel D 2 A section of the Acquisition panel of the FT EPR Parameters window is labeled PulseSPEL Acquisition There are five boxes in this section for the display and selection of parameters for a PulseSPEL acquisition FTEPR Parameters Patterns l Field l RF Acquisition l Scan ABSCISSA QUANTITIES AND SIZES X Axis Quantity Time y X Axis Size 512 Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables amp Run from PulseSPEL wv Read Transient Quadrature Detection E v Start Transient PulseSPEL ACQUISITION PulseSPEL Program SPEL2 fidcycle_bcstep exp Experiment EXP y PulseSPEL Variable d0 40 ns Phase Cycling LISTS y Phase Program Normal y Cose PulseSPEL Help Figure D 2 PulseSPEL Acquisition section PulseSPEL This box indicates the presently loaded PulseSPEL program Program Loading and compiling the programs is described in Section D 3 Experiment This box displays the presently active experiment Click the tri angle on the right side and a drop down menu appears display ing the different experiments defined in the loaded PulseSPEL program Choose the experiment you wish to perform by click ing its name in the list E 580 User s Manual D 21 The PulseSPEL Acquisition Panel Phase Cycle PulseSPEL Variable Phase Program This box displays the presently active pha
91. Microwave Connections Sample Access y If you are perform ing cryogenic exper iments you should periodically check the o ring for wear to avoid air leaks into the cryostat In order to keep the top of the probehead support warm during very low temperature operation there are two water connections to circulate warm water in the top If you are using an ER 4118CF cryostat the extra warming is not needed usually and you do not need to connect the water lines Tell tale signs that things are getting too cold are increased effort to move the coupling adjustment during cryogenic operation and air leaks into the cryostat If you wish to use the water connections con nect two 4 mm Legris tubes to the resonator support Then con nect the other end of each tube so that the bridge and support water supplies are in parallel There are two female SMA microwave connectors one at the top and one at the bottom These connections are described in greater detail in Section Section A 2 and Section A 4 Male Female Figure A 3 Male and female SMA microwave connectors The sample access area consists of three parts the collet nut collet and an 8x1 5 mm o ring The o ring seals around the sam ple rod by tightening the collet nut aa Collet Nut Collet T Figure A 4 Parts for sample access A 6 Resonator Description The Resonator Module A 1 2 The resonator modules each have modulation pins
92. ND SIZES X Axis Quantity Time y X Axis Size 512 m Y Axis Quantity Magnetic Field y Y Axi 2 7 m soo X Axis Size Run from Tables Window v from PulseSPEL m w Re v stat Run from seo Tables Button PulseSPEL Experiment EXP x PulseSPEL Variable Phase Cycling LISTS y Phase Program Normal y Qose PulseSPEL Help Figure 5 25 The Acquisition panel 10 Select Run from Tables Verify that the Run from Tables option is selected in the Acquisition panel Press the Run button See Figure 5 5 The spec trometer then acquires the field swept spectrum and it appears in the viewport Store the spectrum Phase the data The real data should be an exponential decay See Figure 5 26 and the imaginary data should be flat If you followed the directions in Section 5 2 cor rectly phasing should not be necessary If there is an appreciable amount of the decaying exponential signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat E 580 User s Manual 5 23 T2 Measurements T 0 1000 2000 3000 4000 6000 7000 Time ns 5000 Figure 5 26 The echo decay of the coal sample 11 8000 Fit a decaying exponential to measure T3 Click the Exponential Decay command in the Exponentials submenu of the Fitting subnenu The Exponential Decay dialog box appears Click the Fit button and the program will
93. R Eaton S S Eaton and K Ohno Eds CRC Press 1991 Electron Paramagnetic Resonance S S Eaton and G R Eaton in Analytical Instrumentation Handbook Ed G W Ewing Marcel Dekker 2nd ed 767 862 1997 Principles of Electron Spin Resonance N M Atherton Ellis Horwood Ltd 1993 E 580 User s Manual 2 69 Bibliography Electron Paramagnetic Resonance J A Weil J R Bolton J E Wertz John Wiley amp Sons 1994 Echo Phenomena in Electron Paramagnetic Resonance Spectros copy A Ponti and A Schweiger Appl Magn Reson 7 363 1994 Creation and Detection of Coherences and Polarization in Pulsed EPR A Schweiger J Chem Soc Faraday Trans 91 2 177 1995 Phase Cycling in Pulse EPR C Gemperle G Aebli A Schweiger and R R Ernst J Magn Res 88 241 1990 Distortion Free Electron Spin Echo Envelope Modulation Spectra of Disordered Solids Obtained from Two and Three Dimensional HYSCORE Experiments P H fer J Magn Res A111 77 1994 Generation and Transfer of Coherence in Electron Nuclear Spin Systems by Non ideal Microwave Pulses G Jeschke and A Schweiger Molecular Physics 88 2 355 383 1996 Matched Two Pulse Electron Spin Echo Envelope Modulation Spectroscopy G Jeschke and A Schweiger J Chem Phys 105 6 2199 2211 1996 2 70 i Bibliography Pulsed ENDOR The Generalized Hyperfine Sublevel Coherence Transfer Exper iment in One an
94. Reduce the number of points or the number of pulses in order to successfully complete your experiment E 580 User s Manual C 7 The Field Panel The Field Panel C 3 Tan 3480 000 E E 3480 00 a joo ie Figure C 8 The Field panel Field Position The present magnetic field value Its value can only be set within the range defined by the Center Field and the Sweep Width Center Field The value of the center magnetic field Sweep Width The magnetic field sweep width Left Clicking this button sets the magnetic field to the lowest value defined by the Center Field and the Sweep Width Center Field Sweep Width 2 C 8 BRORER The Field Panel Center Right Clicking this button sets the magnetic field to the Center Field Clicking this button sets the magnetic field to the highest value defined by the Center Field and the Sweep Width Center Field Sweep Width 2 E 580 User s Manual The Acquisition Panel The Acquisition Panel Patterns Field Acquisition ABSCISSA QUANTITIES AND SIZES X Axis Quantity Time y X Axis Size 1024 fa al Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE Run from Tables Quadrature Detection J wv Run from PulseSPEL wv Read Transient wv Start Transient PulseSPEL ACQUISITION PulseSPEL Program Experiment lt none gt y PulseSPEL Variable Phase Cycling y Phase Pro
95. T EPR Parameters window There are 26 delay variables DO D31 Pulses are variables that determine the length and source of a PatternJet pulse The variable values pulse lengths can be defined in the variable definitions file in the program through algebraic operations and via editing in the Acquisition panel of the FT EPR Parameters window There are 32 delay variables PO P31 The variables are followed by a set of square brack ets with a definition of the PatternJet channel pl x p0 phi p8 U1 The definition may be a microwave pulse channel a phase pro gram from the lists section or a spare PatternJet channel that can be used to trigger an external device such as a laser If you have an optional pulse ENDOR accessory the definition between the square brackets is slightly different The first entry is either RF 1 or RF 2 and is required to select the desired channel of the ENDOR unit You may also specify a fre quency variable or a phase program but not both after the chan nel designation The following are valid RF pulse definitions sD BROKER EDL The PulseSPEL Programming Language Acq Dig Algebraic Operations P10 RF 2 Pll RF 1 rfpl PL2 CRE 1 dE 1 If you use more than one RF pulse and specify a phase program in at least one of the pulses each RF pulse must have a phase program specified The acquisition command initiates a single point or integrator measurement by t
96. Test 13 Set the offsets for the two channels Use the slider bars to move the two traces up or down See Figure 3 19 The Channel 1 slider should be slightly to the right and the Channel 2 slider slightly to the left This ensures that the two traces will not overlap Figure 3 19 Non overlapping traces showing the defense pulse BkORER Safety Test 14 Look for the defense pulse It should be a sudden change in level in either or both channels See Figure 3 19 If you do not see the defense pulse first change the Signal Phase with its slider bar Microwave Bridge Tuning Si gnal Frequency Bias sas Phase Bes v Tune lt gt Operate Signal Phase LE p Auto Tuning v p v Fine v Down gt Stop Reference Am on voff Dual Trace 7 Attenuation dB 60 0 Reference Arm On Bree Monitoring Close Help Figure 3 20 The Signal Phase slider bar If you still do not see a defense pulse verify that the Ref erence Arm is on and the Bias slider is completely on the right hand side Verify that the LED on the AMP but ton is lit See Figure 3 10 Never switch the TWT to operate If you are still unsuccessful in seeing the defense pulse do mode unless you not continue to the next step Contact your local Bruker h th i Neri i EPR representative for assistance defense pulse If
97. The other trace is the normal tuning mode See Figure 3 7 Tuning Up Resonator modules with two windows will actually operate in the opposite sense Up decreased coupling Down increased coupling The probe head support has a label indicating the non standard opera tion The external resona tor has several modes If its dip looks very broad adjust its frequency until you find a nar row dip This is the correct mode 6 Make sure the resonator is not overcoupled Move the coupling adjustment arm downwards Increased Coupling Decreased Coupling Figure 3 6 The coupling adjustment arm 7 Find the resonator dip Use the frequency slider to center the resonator dip 8 Find the external stabilizer dip Pressing the stabi lizer frequency adjustment buttons changes the external stabilizer frequency See Figure 3 3 Align the external stabilizer and resonator dips together See Figure 3 7 r Frequency 4s y v Stand By Bias ene lt a y Vv operate aas JL p Ba Auto Tuning ie v Up v Fine E apt v eva A Stop Reference Am gt f Sul von off Attenuation dB Dual Trace 7 2 _ g Log Scale _ Options Iris Al yi Monitoring Figure 3 7 The external stabilizer and resonator dips E 580 User s Manual 3 5 Tuning Up Sample position is very important Con sult Appendix A for details
98. We encourage you to tell us how we are doing Please send us your suggestions for improvements corrections or bug reports If there is anything you particularly liked tell us as well With your input and assistance Bruker can continually improve its products and documentation You can send your messages and correspondence via e mail FAX telephone or mail It is important to include the document name product name version number and page number in your response Here are the addresses and numbers to which you can send your messages epr_applications bruker biospin com 978 670 8851 978 667 9580 EPR Division Bruker BioSpin Corporation 19 Fortune Drive Manning Park Billerica MA 01821 USA Thank you for your help E 580 User s Manual Electrical Safety Electrical Safety 0 1 Do not remove any of the protective covers or panels of the instrument They are fitted to protect you and should be opened by qualified service personnel only Power off the instrument and disconnect the line cord before starting any cleaning work in the spectrometer Never operate the instrument with the grounding cord disconnected or by passed Facility wiring must include a properly grounded power receptacle Chemical Safety 0 2 Individuals working with hazardous chemicals toxic substances or enclosed liquid samples must take every precaution possible to avoid exposure to these agents As a general rule THINK OF THE CHEMICAL LABOR
99. aging Zero Filling Fitting FFT Structure area prFFT2D 2D FFT ras wanes oo ProDeL Cross Term Averaging Automati Convolition Je EE Transfori anes R undo Deeanvolution i Symmetrization Invert Abscissa g Factor Transform SQRT of Abscissa Button Normalize Axes Figure 7 22 The FFT command 28 Click the Transform button The default options are appropriate for what we are doing The result will appear in the Primary dataset E 580 User s Manual 7 19 The HYSCORE Experiment 29 Select the Absolute button in the Complex sub menu of the Processing menu The software will calculate the magnitude spectrum of our complex data Processing Diff amp Integ ig Absolute Filtering Algebra Command Peak Analysis Complex Window Functions Transformations imagini Fitting Structure r XSophe ProDeL B Aurtamatic Re lt gt m Conjugate Figure 7 23 The Absolute command 30 Select the Normalize Axes command in the Com plex submenu of the Processing menu GHz is not the most sensible unit for ESEEM This command con verts it to the more sensible MHz Processing Diff amp Integ Filtering Algebra Peak Analysis ra Complex Ea Window Functions imaging 7 Zero Pling a 7 Fitting _ FFT Transformation Structure _ FFT Real
100. an els See Figure C 1 Each is activated by clicking the button Closes the FTEPR Parameters window This also closes the PulseSPEL editor display when clicked Invokes the PulseSPEL editor See Appendix D Invokes the Xepr help system to assist you with questions Many of the editable boxes have arrows next to them When clicked they work as follows Increments the parameter value Decrements the parameter value When the lt Ctrl gt key is pressed simultaneously while clicking an arrow the parameter changes in a coarse step size When the lt Shift gt key is pressed simultaneously while clicking an arrow the parameter changes in an even coarser step size E 580 User s Manual The Patterns Panel The Patterns Panel C 2 The Patterns panel groups together the parameters required to determine the timing of pulse experiments It is also often referred to as the Pulse Tables Figure C 1 The Patterns panel Shot Rep Time The shot repetition time It is the time interval at which experi ments are repeated i e the reciprocal of the repetition rate Shots Per Point The numbered of times a signal is averaged by repeating a pulse pattern without any change in the pulse timing or magnetic field position C 2 BRORER The Patterns Panel Channel Selection When clicked a drop down menu appears in which the various pulse channels of the PatternJet pulse programmer are listed Click the des
101. and in the Acquisition menu Click the FT EPR tab to view the Configuration and Timing panel Acquisition Processing Viewports i New Experiment Select Experiment i Experiment Parameters Show Description Get Parameters From Experiment Get Parameters From Dataset Create Experiment Link Remove Experiment Link Microwave Bridge Tuning Set Sample Info Spectrometer Configuration Panel Properties Auto Connect To Spectrometer Connect To Spectrometer Disconnect From Spectrometer Auto Post Processing Check Post Processing Set Parameters from Display Tools Experiment Table Figure E 1 The Acquisition menu E 580 User s Manual Spectrometer Configuration Spectrometer Configuration E 1 There are six buttons that the Configuration and Timing panel shares with the other panels The most important is the Apply button because no changes are activated until it is clicked DATA SET SELECTION PULSE PROGRAMMER SETUP Figure E 2 The Configuration and Timings panel E 2 BRORER Configuration and Timing Close Closes the Spectrometer Configuration panel Apply Activates the present spectrometer configuration Reset Resets all the values to the original values Load Loads a new configuration file Save Saves anew configuration file Configuration and Timing E 2 A These values a
102. annel b i signprogr Re Im a b iy a b Pe r i b a h a b a jiu ff AE ra Pee es ee 0 400 800 1200 1600 2000 Ins Changes in the FID during a four step phase cycle The next two steps require application of a y or y pulse This then exchanges the signal that originally was in channel a with the channel b signal We now add and subtract the channel b sig nals with our previous real results and the channel a signals with the imaginary results These two steps suppress the aliasing arte 2 64 BROKER CoD Pulse EPR Practice facts because we have sent identical signals through both chan nels a and b now thus averaging the gain and reference phase imbalances to approximately zero After Fourier transforming the FID we now obtain a nice spectrum with no artefacts See Figure 2 66 Re Im xk QUAD ON Astep 9 rot QUAD ON 2step rot QUAD ON i QUAD OFF Pop a i Ps ep 60 50 40 30 20 i0 0 10 20 30 40 50 60 MHz Figure 2 66 The effect of the four step phase cycle upon the frequency spectrum E 580 User s Manual 2 65 Pulse EPR Practice Unwanted Echoes We saw in Figure 2 40 that three microwave pulses create five amp FIDS echoes In a three pulse ESEEM experiment we are only inter ested in the stimulated echo The other echoes only give us arte facts as they run through our stimulated echo There is a phase cycle that leaves the stimu
103. apter The rotating frame also makes the magnetization components precessing at the Larmor frequency to appear stationary Using Equation 2 1 and assum ing the magnetization is not precessing in the rotating frame 0 the field By disappears in the rotating frame In the rotating frame we need only to concern ourselves with a station ary Byand Mo Lab Rotating Frame Frame Figure 2 4 The microwave magnetic field in both reference frames E 580 User s Manual 2 7 Pulse EPR Theory w For a given tip angle as B gets larger the pulse length gets shorter We have already looked at the interaction of a static magnetic field with the magnetization the magnetization will precess about B at a frequency yB 2 3 where is also called the Rabi frequency Let us assume that B is parallel to the x axis The magnetic field will rotate the magnetization about the x axis as long as the microwaves are applied See Figure 2 5 Figure 2 5 Rotating the magnetization The angle by which Mg is rotated commonly called the tip angle is equal to a y By tp 2 4 where t is the length of the pulse Pulses are often labeled by their tip angle i e a 2 2 pulse corresponds to a rotation of My by 1 2 The most commonly used tip angles are 1 2 and x 90 and 180 degrees The tip angle is dependent on both the magnitude of B and the length of the pulse For example a B4 of 10 Gau
104. as one broad signal See Figure 2 17 Typically this type of broadening results in a Gaussian line shape which we shall discuss in the next section This distribution of local fields gives us a large number of spin packets characterized by a distribution of Aw in the rotating frame As shown in Figure 2 10 the magnetization of an indi vidual spin packet will rotate if Aw 0 and the larger Aq is the faster it rotates If we sum up all the components of the individ ual spin packets we see that many components cancel each other out and decrease the transverse magnetization See Figure 2 18 The shape of this transverse magnetization decay actually a FID is in general not an exponential decay but instead reflects the shape of the EPR spectrum The characteris tic time constant for the decay is called T T two star ang Kx aK SR Figure 2 18 Fanning out of the transverse magnetization and the decrease of the trans verse magnetization 2 20 Pulse EPR Theory y Unlike the static effects of inhomoge neous broadening homogeneous broad ening results from random and irrevers ible events This fact will become impor tant when we discuss spin echoes In Figure 2 17 each of the individual spectra or spin packets which comprise the inhomogeneously broadened line are homo geneously broadened In a homogeneously broadened spectrum all the spins experience the same magnetic field The spi
105. ase programs that can be defined for the micro wave pulses PHO PH15 A phase program consists of an identifier such as PH1 in our example program followed by a list of microwave pulse channels Valid pulse channels are X lt X gt X lt X gt Y lt Y gt y lt Y gt CWarm Depending on the number of MPFUs in your bridge not all channels may be valid for your spectrometer The asterisk denotes a skipped or null pulse Each phase program is a list that defines the sequence of phases used in a phase cycle If you have an optional pulse ENDOR accessory you can also phase cycle the RF There are 16 phase programs that can be defined for the RF pulses RFPO RFP15 A phase program consists of an identifier such as RFPO followed by a list of RF phases Valid entries are 0 90 180 270 There are 8 sign programs for both the real and imaginary com ponents of the dataset ASGO ASG7 and BSGO BSG7 Sign programs are defined in a similar way to phase programs Valid entries for the sign program are A A B B where A and B denote data from the first and second channel of the quadrature detection and the asterisk a null or skipped acquisition The sign indicates whether the data is to be added or subtracted from the dataset E 580 User s Manual The PulseSPEL Programming Language As an example let us look what happens in the following four step phase cycle begin lists phil x
106. ation is precessing at Aw and therefore By Ao 2 6 y B o 0 Y pn eff a S AU B y A M x Figure 2 11 The effective microwave magnetic field in the rotating frame 2 12 Pulse EPR Theory in the rotating frame Now the magnetization is not tipped by B but by the vector sum of B and Bg which is called Begg or the effective magnetic field The magnetization is then tipped about Betr at the faster effective rate O grr Oe Jo 40 2 7 lt 6 Another consequence is that we cannot tip the magnetization Q i into the x y plane as efficiently because Beg does not lie in the x y plane as B4 does The magnetization does not move in an arc as it does on resonance but instead its motion defines a cone In fact it can be shown that the magnetization that can be tipped in The tip angle is then a function of the off set Aw The 7 2 tip the x y plane exhibits an oscillatory and decreasing behavior as angle is only strictly Ao gets larger valid exactly on res onance l A T M My sin 1 7 2 8 1 22 Oy 2 r fo 10 8 6 4 2 0 2 4 8 10 Aw o Figure 2 12 The transverse magnetization as a function of the offset after a 2 2 pulse E 580 User s Manual 2 13 Pulse EPR Theory One thing is evident from Figure 2 12 if we have a very broad qy EPR spectrum Ao gt 1 we will not be able to tip all the mag a netization into the x y plan
107. attenuator settings when you were using your coal sample you probably do not have to worry about optimizing all the parame ters The best approach is to first acquire an echo detected field swept EPR spectrum using the instructions in Section 5 5 2 You can use the PulseSPEL variable values and HPP attenuator setting you determined in Section 5 5 1 while using the strong coal sig nal Set the Center Field and Sweep Width to values at which you expect to observe your EPR signal You will need to maxi mize the VAMP gain and set the number of averages to a fairly high value gt 1000 The number of averages is probably best increased by keeping h 100 and increasing n to ten or greater Once the dataset is acquired you will then need to phase it prop erly with the software Once you have an EPR spectrum you can then decide at which field you wish to perform further experiments In most cases these experiments require the value of dO in order to digitize the height of the echo We already have this value from Section 5 5 1 There are a few cases where this approach may not succeed l If you change the VAMP bandwidth the timing for acqui sition trigger changes E 580 User s Manual 5 45 Advice for Real Samples If you are working with an electron spin system with S gt 1 2 the HPP attenuator setting and acquisition trigger timing may no longer be appropriate If you have strong ESEEM you may have to choose anothe
108. back views of the ER 4118 SPT probehead support Modulation Wires Ad ie Resonator Description Thermocouple The probehead support is fitted with a Chromel Alumel K type thermocouple located next to the resonator module There is a twin ax BNC connector on the upper body of the support Using the supplied thermocouple cable you can measure the tempera ture with an ER 4131 VT temperature controller If you use the optional ER 4118CV cryostat you can also control the tempera ture with this thermocouple Modulation The twin ax BNC connector labeled Mod is the connection for field modulation It should be connected to the modulation cable coming from the console On the bottom of the support are two wires with connectors on the end which supply the resonator module with field modulation Coupling The lever arm with the thumb screw adjusts the coupling or Adjustment match of the resonator Moving the lever arm up increases the coupling and moving the lever arm down decreases the cou pling Turning the thumb screw counter clockwise moves the lever arm up and turning the screw clockwise moves the lever arm down Resonator modules with two windows will actually operate in the opposite sense Up decreased coupling Down increased coupling The probe head support has a label indicating the non standard opera tion E 580 User s Manual A 5 Resonator Description Water Connections
109. bar The subtraction result appears in the Result dataset 16 Transfer the Result to Primary Click the Primary dataset selector and click on lt Result gt This transfers the Result dataset to the Primary dataset for further process ing 17 Interchange the axis direction We are presently baseline correcting slices parallel to the t axis We need to baseline correct in the t direction as well Click the interchange axes button Interchange annn my Axes Button Late ents ae eet sje EI 0 500 1 000 1 500 2 000 Intensity Viewport 1 Time ns Time 0 ns Figure 7 18 Interchanging the axes 18 Repeat Step 13 through Step 16 19 Click the Return button See Figure 7 16 The HYSCORE Experiment 20 Click the Window Function task button The Win dow Function task bar then appears TASKS WINDOW FUNCTIONS Baseline Correction Window Start Peak Picking Function mT Integration Button FFT Real gt Fitting ERONEN Filtering Tee Hamming xSophe mises Function Gas Button e Save Statin Beye eea Gas FFT Real lt o em Figure 7 19 The Window Function task bar 21 Click the Hamming button in the Window Func tion task bar The Hamming window dialog box appears prWinHamming Slice current v all x Max pass O maa p Ae Apply Window Function Clo se Button y 0 54 0 46 cos Prs Button
110. button The pulse program is not only compiled but also each step is checked to verify that it is within the lim its of the spectrometer capabilities If successful the state E 580 User s Manual D 25 Setting up a PulseSPEL Experiment Figure D 6 Close Button Validate Button ment Second pass ended appears in the message window PulseSPEL Programming Panel fidcycle_bestep exp edited dir lusripeopleirtwixeprFilesiPulseSPEL ishare Fle Edit Search Compile Properties Options Hep 3 ay Abort end lists Load Var Def FID detection with transient recorder using CYCLOPS off resonance baseline correction Save Program Save Var Def Show Program begin defs dim s 512 1 Show Var Def ond defs jae begin lists phi x x y y Verbose oniort asgl a a b b on resonance sign program Compile bsgl b b a a Validate asg2 a a b b off resonance sign program bsg2 b b a a begin exp quad trans shot i 1 to 2 dig sg1 next i bestep 200 ff resonance step Message shot i 1 to 2 6 BO phl Window w a y gt Second pass ended E Help On f Selection Validating the PulseSPEL program T Close the PulseSPEL window Double click the close button 8 Edit the PulseSPEL variables Type the variable name in the PulseSPEL Variable box and then press the Enter key The present value for that variable will appear T
111. ccceccceeceeeseeenseceteceteeeeeeeneeens D 21 D 3 Setting up a PulseSPEL Experiment 000 0000 cececcceesseceteceeeeeeeeeeeeeeeeens D 23 D 4 PulseSpel Programming Pane lei isesiesis ssaaeteirsusdosdinasnoasead kesachiaeovbukdoes D 29 DAT HATS carseat castes dvds ida tans iviedea ay bacas ite e dah E E R D 31 D42 Editia len Bd i A bay Nine oy eet ok ats sede dlea tp E D 36 D43 Sear Ganenn a oid das easibleenseas dae eee Mian ae ds eee D 38 DAA Compile eoscs sas cecicus cacacasvectua vsaceeaus fdiwons Cauearg docteed da eins Mae eaate teeaate fatians bata does D 39 D45 Properties sis ron ae eticersgtaeaea icine one has D 40 DAG Options eneinio iiie ives ovsed devel E ons E andes caetivecuseateese D 41 DAT BUON hennis ae aa oaa E ET E A a An anaa D 41 DS Pulse Tables vs PulseS PE Bax ccanaccsciicce an tdccnseataaenaienawne D 42 Appendix E Configuration Table cccccceeeeceeeeeeeeeeeeeees E 1 El Spectrometer Configuration css cassdehtdssersetspendocde sendud euaahadseltvsantivwes E 2 E 2 Configuration and Pim nig ce oss Saccesios oceus Coadastecss seas cats ataceo sess eekeaocase ness E 3 EZ 1 Data Set Sele ctw On enirere e a e ea tt ia i i fee es E 4 E22 TWE and RE a octal eid a a ae ae Hae E 4 E 580 User s Manual xi Table of Contents E 2 3 Pulse Programmer Setup cccccccccccscecssecseceeseseeeseeeeeeeeseecseeeeseeseceeeseeeeneeesaes E 5 Bs Ms grass aan E EA A as eee een Se E 6 Appendix F Phase amp Amplitude Adjustm
112. compilation initializes all the various delays lengths and counters to the default values 6 Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file fidcycle_bcstep exp and click the Load button PulseSPEL Programming Panel deser def dir lusripeopleirtwixeprFilesiPulseSPELisharedPulseSPELiStane File Edit Search Compile Properties Options Load Program 2 is PulseSPEL general variables definitions amp convention Load Var Def Save Program Load Program begin daie Save Var per Button Show Program Feb 2000 PE Show Var Def Variables 4 Comments a po 16 90 pulse length etc pl 32 Renee p2 32 agPgload pai r Gro Contents of this Gro Verbose oniott p 80 me Compile pg Validate do Abort d2 lses lses t ae 0 hyscore_se 4 ae ci PulseSPEL Program Path JsredPulseSPEL Standard PulseSPELZ000 SPELZ Create d30 4 aji 4 File fucycte_bestep exp 1 show Filenames d20 0 d21 0 Gaal Help h 5 unter I 20 number of sweeps to accumulate counter K Sweep length n of data really taken counter X p z Figure 4 10 Selecting the PulseSPEL program 4 10 BkGieR Acquiring a FID with PulseSPEL 7 Validate the PulseSPEL program Click t
113. covers to thermal equilibrium is T the spin lattice relaxation time The magnetization will exhibit the following behavior after a 7 2 pulse M t Mg s 2 10 or after a 7 pulse M t My 1 2 2 11 n 2 Pulse m Pulse Recovery of the magnetization after a microwave pulse E 580 User s Manual 2 17 Pulse EPR Theory In order to extract our signals from the noise we must signal average the FID by repeating the experiment as quickly as possi ble and adding up the individual signals What does as quickly as possible mean We must wait until the magnetization along the z axis has recovered because if there is no z magnetization you cannot tip it into the x y plane to create a FID The first FID will be maximum and the following FIDs will eventually approach a limit value that is smaller than the initial value See Figure 2 16 Winseea See cactaaas Naks aa Ron E m r A 0 2000 4000 6000 8000 10000 12000 14000 16000 18000 20000 22000 Time ns Figure 2 16 Repeating a FID experiment too quickly For best results you should use a Shot Repetition Time of 5x Ty The limit value as a function of T and SRT the Shot Repetition Time which is the time between individual experiments is equal to SRT M SRT Mo 2 12 One important fact is that if SRT 5 x T 99 of the magneti zation will have recovered before the next exper
114. ct for this by a constant i e frequency independent phase correc tion The constant phase correction also corrects for a Signal Phase that is not properly set E 580 User s Manual 4 23 Processing the FID 1 Select the Phase command Click its button in the Transformations submenu of the Processing menu Processing Diff amp Integ Transformation Biter G Algebra Submenu Peak Analysis Complex Window Functions Transformations F nagen Z Zero Filling Fitting _ FFT Structure FFT Real XSophe 2D FFT ProDeL Cross Term Averaging Automatic Convolition undo Deesnvantion 42 G Invert Abscissa g Factor SQRT of Abscis Phase Normalize Axes a Command Normalize Spec Normalize Int S Phase Left Right Shift Polar to Rect Rect to Polar Linear Figure 4 30 The Phase command Na 2 Phase the data Enter a number in the Oth Order box 9 and click the Apply button You can also use the arrows next to it to vary the phase Continue until the data appear properly phased See Figure 4 32 and Figure 4 33 Wi fi i i A E Click the Close button and then the Yes button in the dia the operation described in log box that appears The result is now transferred to the Figure 2 49 here Primary dataset 4 24 ekGaen Processing the FID prPhase Box O
115. cules are too large to perform high resolution NMR experiments Pulse experiments measure relaxation times more directly than CW techniques such as saturation The relaxation time measure ments offer you dynamical as well as distance information for the samples you are studying As interest in measuring longer distances between paramagnetic centers increases the techniques of 2 plus 1 DEER Double Electron Electron Resonance and ELDOR ELectron DOuble Resonance are invaluable in measuring particularly long dis tances in very large molecules Quite often there are events that take place on time scales that do not influence the relaxation times and hence the lineshapes EXSY EXchange SpectroscopY measures rates for slow inter and intra molecular chemical exchange homogeneous electron transfer and molecular motions 2 2 Pulse EPR Theory Pulse EPR Theory 2 1 Though Pulse EPR may seem a bit daunting in the beginning there are a few simple principles that help you understand pulse EPR experiments The first important principle to master is the rotating frame Since Pulse EPR involves going between the time and frequency domains we shall also discuss some of the important relations in Fourier theory You will find that we will often use these simple principles throughout the coming chap ters The treatment is not mathematical but intended to give you an intuitive understanding of the phenomena The Rotating Frame 2 1
116. d Two Dimensions M Hubrich G Jeschke and A Schweiger J Chem Phys 104 6 2172 2184 1996 Pulse Schemes Free of Blind Spots and Dead Times for the Mea surement of Nuclear Modulation Effects in EPR J Seebach E C Hoffmann and A Schweiger J Magn Res A116 221 229 1995 Primary Nuclear Spin Echoes in EPR Induced by Microwave Pulses E C Hoffmann M Hubrich and A Schweiger J Magn Res A117 16 27 1995 Nuclear Coherence Transfer Echoes in Pulsed EPR A Ponti and A Schweiger J Chem Phys 102 13 5207 5219 1995 J P Hornak and J H Freed J Magn Res 67 501 518 1986 2 3 3 Pulsed ENDOR Experiments W B Mims Proc Roy Soc 283 452 1965 A New Pulsed ENDOR Technique E R Davies Phys Lett 47A 1 1974 ENDOR Spin Echo Spectroscopy A E Stillman and R N Schwartz Molecular Physics 35 301 1978 E 580 User s Manual 2 71 Bibliography Bloch Siegert Shift Rabi Oscillation and Spinor Behaviour in Pulsed ENDOR Experiments M Mehring P H fer and A Grupp Phys Rev A33 3523 1986 High Resolution Time Domain Electron Nuclear Sublevel Spectroscopy by Pulsed Coherence Transfer P H fer A Grupp and M Mehring Phys Rev A33 3519 1986 Pulsed Electron Nuclear Double and Triple Resonance Schemes M Mehring P H fer and A Grupp Ber Bunsenges Phys Chem 91 1132 1987 Multiple Quantum ENDOR Spectroscopy of Protons in Trans Polyacetylene M Mehring P
117. d and Sweep Width parameters bsweep x 1 to sx Shot i g toh some commands next i next x The loop variable must be x The loop counter must start at 1 The Sweep Width is separated into equally spaced intervals The PulseSPEL Programming Language Rfsweep Bcstep Sleep Scansdone k Totscans n The last type of loop sweeps the RF for a pulse ENDOR experi ment The syntax of this loop is different from the other loops because of the manner in which the x axis is defined rfl dfl start frequency dx rfl assignment of x axis rfsweep x 1 to sx Shot i g toh some commands next i rfl rfl dfll increment rfl by qdf11 dx dx dfll determine x axis next x The loop variable must be x The loop counter must start at 1 The extra statements defining dx are required in order to prop erly generate the x axis The bestep command offsets the Center Field by the specified value For example bcstep 200 will decrease the Center Field by 200 G The sleep command causes the acquisition to pause or wait for the specified amount of time For example sleep 10 will cause the program to wait for 10 seconds This command is particu larly useful after a bcstep command because it may take a bit of time before the field is stabilized Displays the present value of the loop variable k in the message window of the Xepr window Displays the upper loop limit n in the message window of the Xepr win
118. d31 next y end exp egin defs dim s 150 150 end defs f L begin lists PRL x x x x ph2 x x x X asgl ta a bsgl b a a b b p end lists L r begin exp SPT QUAD dx 0 dy 0 for y 1 sweep shot po d1 po d2 dy p2 d3 dx po to sy x to sx i l to h x x ph1 ph2 do acq next sg1 i dx dx d30 next x dx 0 dy dy d31 next y end exp Figure 7 12 Original left and modified right PulseSPEL programs for HYSCORE Added and modified sections are highlighted E 580 User s Manual 7 11 The HYSCORE Experiment 5 Validate the edited PulseSPEL program Click the Validate button The pulse program is not only compiled but also each step is checked to verify that it is within the limits of the spectrometer capabilities If successful the statement Second pass ended appears in the message window 6 Close the PulseSPEL window Double click the close button po po p2 po Acquisition 5 5 z Z Trigger in i d1 t d2 i d3 tot d1 t do 1 Figure 7 13 Variable definitions for the modified hyscore exp 7 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 7 13 Set the variables to the values indicated in Table 7 2 i The HYSCORE Experiment 10 Variable Value d1 128 ns d2 200 ns d3 200 ns dO Determined in Step 14
119. dary gt a gt F fno Result gt Y fo Qualifier gt 10 000 Re Im 10 000 Button 5 000 5 000 0 AT ey See ee 0 1 Viewport eae ea Selection Bar 10 000 10 000 sido D 0o S RA 5 1500 omy 2 000 som H i 500 7 1 000 T T 2o00 Intensity Viewport 1 Time ns Intensity J Viewport 3 Time ns Figure 4 16 Displaying both real and imaginary components of the FID 3 Click the Baseline Correction task button fol lowed by the Polynomial task button The polyno mial baseline correction task bar then appears TASKS jaseline Correction Peak Picking Integration Fitting Window Function Filtering XSophe eae eet BS Baseline Correction Button BASELINE Polynomial Spline Retum Polynomial Button Figure 4 17 Selecting polynomial baseline correction E 580 User s Manual 4 15 Processing the FID 4 Select the real trace Click its viewport selection bar to activate it N 5 Mark the baseline of the real trace Click the Define b Region button This action sets the cursor into the region qualifier mode Qualify the flat sections of the FID Note that both the BASELINE POLY real and imaginary parts are qualified J The two viewports OO O are linked Define Eee Region _1 oth Order HGS Button Button Ronn e Sub Li tract Line Seene 7 aa Button Return Subtract Line ay a em
120. dout E 580 User s Manual 5 21 T2 Measurements 3 Enter the Acquisition Trigger position and posi tion displacement Enter the time determined in Step 2 into the Acquisition Trigger Position box Enter 16 ns into the Pos Disp Position Displacement box This position displacement successively increases the position of the Acquisition Trigger by 16 ns FTEPR Parameters Patterns l Field RF Acquisition Scan Options PULSE PATTERNS Channel Selection Acquisition Trigger Shot Rep Time us 999 60 Integrator Time Base ns Single Point y Shots Per Point 10 Edit Position ns Length ns Pos Disp ns Length Inc ns Cose PulseSPEL Help Figure 5 24 Programming the position displacement for the Acquisition Trigger 4 Set the x position displacement of the second x pulse Enter 8 ns into the Pos Disp box of the sec ond x pulse This position displacement successively increases the spacing between the two microwave pulse in steps of 8 ns 5 Set the Shoots Per Loop This value specifies the number of times the signal is averaged Set it to 100 See Figure 5 24 5 22 T2 Measurements 6 Set the X Axis Size Set the value to 512 FT EPR Parameters Pattems Field RF Acquisition l Scan Options ABSCISSA QUANTITIES A
121. dow E 580 User s Manual D 13 The PulseSPEL Programming Language An Example D 1 4 Perhaps the easiest way to learn about PulseSPEL is to look at the standard Bruker PulseSPEL programs Here is a simple experiment to acquire a two pulse echo standing echo Ne Ne Ne Ne Ne begin defs dim s 512 1 end defs r r begin lists phl x x asgl ta a bsgl b b end lists 7 7 begin exp SPT QUAD for k 1 to n sweep x 1 to sx shot i l toh po phi d1 pl x dl do dx acq sgl next i dx dx d30 next x dx 0 r Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne program to evaluate timing for 2 puls two step phase cycle to eliminate FID after 2nd pulse cho experiment dimension of data array sx sy phase program for 1st pulse sign program for RE part sign program for IM part Single Point QUAD detection averaging loop sweep loop accumulation loop lst pulse and phase program tau 2nd pulse tau constant acquisition delay increment trigger position acquisition end of accumulation loop increment trigger position by d30 end of sweep loop scansdone k output of scans done totscans n output of total number of scans next k end exp D 14 akGien The PulseSPEL Programming Language We set the size of our dataset with the dim s 512 1 statement We define a phase and sign program in the lists section Quadra ture detection with single point detection is chosen w
122. ds If we make t long enough we can ensure that the echo appears after the deadtime How does the echo bring back our signal The decay of the FID is due to the different frequencies in the EPR spectrum causing the magnetization to fan out in the x y plane of the rotating frame When we apply the z pulse we flip the magnetization about the x axis The magnetization still rotates in the same direction and speed This almost has the effect of running the FID backwards in time The higher frequency spin packets will have travelled further than the lower frequency spin packets after the first pulse However because the higher frequency spin packets are rotating more quickly they will eventually catch up 2 34 W J A m a Pulse EPR Theory with the lower frequency spin packets along the y axis after the second pulse See Figure 2 35 n Pulse Figure 2 35 Refocusing of the magnetization during an echo After all the spin packets bunch up they will dephase again just like a FID So one way to think about a spin echo is a time reversed FID followed by a normal FID Therefore if we Fou rier transform the second half of the FID we obtain the EPR OR RD ke Che fers Oe Figure 2 36 Magnetization behavior during an echo experiment E 580 User s Manual 2 35 Pulse EPR Theory y Quite often the echo decay is not a sim ple exponential owing to the many processes that can contrib
123. e The FIDs and echoes are very low level signals so we need a preamplifier to lift them up out of the noise This is a bit tricky however because we are using high power microwave pulses and the reflected pulses as well as the resonator ringdown one of the causes of the so called deadtime can easily burn out our preamp To avoid destroying it we use a PIN diode switch known as the defense diode to block the high power micro wave pulses from reaching the preamp We cannot measure the 2 44 i Pulse EPR Practice signals until the high power microwaves are dissipated and we can turn the defense diode on again See Figure 2 47 gt Deadtime gt Defense Pulse Figure 2 47 The defense pulse and the deadtime The amplified signal then proceeds to the quadrature detector Quadrature detection is simply an electronic means for measur ing both transverse magnetization components in the rotating frame This gives us the required amplitude and phase informa tion to transform the signals into a frequency representation See Figure 2 48 and Figure 2 19 Av 90 signal v Av Im 90 lt i fo lt N Av 90 DXI L Av 0 A i A ff y Re 0 Av 0 90 Z J 1 a B _ reference v 9 10 GHz Av 0 200 MHz Figure 2 48 Quadrature detection E 580 User s Manual 2 45 Pulse EPR Practice The outputs from the quadrature detector correspond to the real
124. e COS ot 5 g 5 p 0 b b ts A aa o Sin ot 0 5 q 0 00 e ee et T2 1 T3 26 1 T 5 1 T d 0 t gt 0 wal o ert 12 e 1207 ee 1207 erf o 202 e 1 Qt t gt 0 0 n t r O t t Sin t o 0 Figure 2 21 Useful Fourier transform pairs For simplicity F normalization constants are omitted E 580 User s Manual 2 25 Pulse EPR Theory Fourier Transform One important property that we shall need is that the Fourier Properties transform of the sum of two functions is equal to the sum of the Fourier transforms f t g t lt gt F Go 2 21 f t F a aaah pare a a WI aa a ae Figure 2 22 The addition property of the Fourier transform Another important property is how the frequency domain signal changes as we time shift delay or advance the signal in time the time domain signal or how the time domain signal changes if we frequency shift the frequency domain signal After a bit of math we obtain the following Fourier transform pairs f t At S F e 2 22 f t i t amp F Ao 2 23 Cos J J A m a 2 26 Pulse EPR Theory When time shifting we obtain the original frequency domain signal with a frequency dependent phase shift As we can see from Figure 2 23 the phase shift transfers some of the real sig nal to the imaginary and vice versa This effect leads to the well known linear phase distortion and correctio
125. e we will see a single decaying exponential Depending on the Signal Phase we will see the signal in both quadrature channels See Figure 4 2 Use the Field Position and not the Center Field to adjust the field This gives you faster and more precise control of the field 10 000 5 000 5 000 y 10 000 0 500 1000 1500 2 000 0 Time ns Figure 4 2 Anon resonance FID Adjust the sample height If your DPPH sample does not have the DPPH crystal position clearly marked you may have to move you sample up and down to properly center it in the resonator for maximum signal intensity If you rotate the sample as you raise and lower the sample you will see the sample go in and out of resonance This is because of the g anisotropy of DPPH Repeat Step 4 if this happens E 580 User s Manual Acquiring a FID with the Pulse Tables 6 Adjust the Signal Phase so that the FID is only in one channel You do not have to get everything perfect we shall see in Section 4 3 4 that we can correct the phase later with the processing software Microwave Bridge Tuning Frequency lt 4 p gt v Stand By v Tune Operate Bias lt P 1 p Signal Phase lt __ ee p Auto Tuning io e Fine Phase Slider Reference Am Dual Trace 7 On voff Attenuation dB I 60 0 Log Scale _J ris Al Y Ea Optio
126. e 4 34 A magnitude spectrum of the Section 4 2 dataset To calculate the magnitude spectrum click the Absolute button in the Complex submenu of the Processing menu Processing Diff amp Integ Filtering Algebra Peak Analysis Complex es Window Functions Absolute Transformations Power imaging _ Real Part Fitting Imag Part Structure _ Re lt gt m XSophe Conjugate ProDeL Buki Complex Automatic Figure 4 35 The Absolute command E 580 User s Manual 4 27 Notes 4 28 Two Pulse Experiments 5 There are two types of two pulse experiments The first is either a saturation or inversion recovery experiment with FID detec tion The second type consist of various echo experiments Two samples for pulse experiments are supplied with each Bruker E 580 spectrometer a DPPH and a coal sample The DPPH has a line width of about 1 G and a very short T and T3 Because of the short relaxation times no echo can be observed The coal sample has a linewidth of about 5 G a longer T gt and a much longer T Because of the broader linewidth most of the FID from the coal sample decays away before the deadtime ends Therefore we shall use the DPPH sample for the FID detected inversion recovery experiment and the coal sample for the echo experiments The inversion recovery experiment measures the T or spin lat tice relaxation time of the sample See Section 2 1 2 An
127. e Ne Ne QUAD detection accumulation loop DAF lst pulse and phase program tau 2nd pulse and phase program tau constant acquisition delay acquisition end of accumulation loop INTG QUAD QUAD detection averaging loop totscans n output of total number of scans bsweep x 1 to sx 7 sweep loop shot i l toh accumulation loop d9 DAF p0 ph1 lst pulse and phase program dl tau pl ph2 2nd pulse and phase program dl tau do constant acquisition delay acq sgl acquisition next i end of accumulation loop next x 7 end of sweep loop scansdone k output of scans done next k D 18 okGien The PulseSPEL Programming Language end expl 2 Pulse ESEE begin exp2 for k 1 to n totscans sweep x 1 to sx shot i l to h dg pO phi d1 dx p1 ph2 d1 do dx acq next i WIE n sgl dx dx d30 next x dx 0 U E3 wn T x Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne scansdone k A next k end exp2 2 Pulse EM vs Field Sweep begin exp3 ey P ES r bsweep y 1 to sy EM INTG QUAD averaging loop output of total number of scans sweep loop accumulation loop DAF lst pulse and tau tau increment 2nd pulse and tau phase program phase program constant acquisition delay increment trigger position acquisition end of accumulation loo
128. e Publications 1992 2 3 2 Electron Paramagnetic Resonance of Transition Ions A Abragam and B Bleaney Dover Publications New York 1970 Transition Ion Electron Paramagnetic Resonance J R Pilbrow Oxford Science Publications 1990 Electronic Magnetic Resonance of the Solid State J A Weil Ed The Canadian Society for Chemistry Ottawa 1987 Structural Analysis of Point Defects in Solids J M Spaeth J R Niklas and R H Bartram Springer Verlag 1992 Electron Spin Echoes W B Mims in Electron Paramagnetic Resonance Ed S Geschwind Plenum Press New York 1972 Time Domain Electron Spin Resonance L Kevan and R N Schwartz Wiley amp Sons 1979 Pulsed EPR A New Field of Applications C P Keijers E L Reijerse and J Schmidt Eds North Holland 1989 2 68 i Bibliography Advanced EPR Application in Biology and Biochemistry A J Hoff Ed Elsevier 1989 Modern Pulsed and Continuous Wave Electron Spin Resonance L Kevan and M K Bowman Eds Wiley amp Sons 1990 Electron Spin Echo Envelope Modulation ESEEM Spectros copy S A Dikanov and Y D Tsvetkov CRC Press 1992 Pulsed Electron Spin Resonance Spectroscopy Basic Principles Techniques and Examples of Applications A Schweiger Angewandte Chemie 3 Int Ed Engl 30 265 292 1991 Electron Nuclear Double Resonance Spectroscopy of Radicals in Solution H Kurreck B Kirste and W Lubitz VCH 1988 EPR Imaging and In Vivo EPR G
129. e to create an FID This is why it is Q important to maximize or equivalently to minimize the 7 2 pulse length for broad EPR signals As B gets larger and the A handy rule of pulse lengths get shorter we can successfully detect more of thumb is that the sig our EPR spectrum See Figure 2 13 nal intensity at Ao will be a factor of two smaller than when Ao 0 for a 1 2 pulse 16 ns 32 ns 48 ns 64 ns r r r T por g r mero 65 60 55 50 45 40 35 30 25 20 15 10 5 0 5 10 15 20 25 30 35 40 45 50 55 60 MHz Figure 2 13 The effect of pulse length on an FT EPR spec trum of the perinaphtheny radical W J A m a 2 14 i Pulse EPR Theory Relaxation Times 2 1 2 Spin Lattice Relaxation Time So far our description is a bit unrealistic because when we tipped the magnetization into the x y plane it remained there with the same magnitude Because the electron spins interact with their surroundings the magnetization in the x y plane will decay away and eventually the magnetization will once more return to alignment with the z axis This process is called relaxation and is characterized by two constants T and T gt The spin lattice relax ation time T describes how quickly the magnetization returns to alignment with the z axis The transverse relaxation time T describes how quickly the magnetization in the x y plane i e transverse magnetization
130. ections are high lighted 6 6 Inversion Recovery with Echo Detection 8 Validate the edited PulseSPEL program Click the Validate button The pulse program is not only compiled but also each step is checked to verify that it is within the limits of the spectrometer capabilities If successful the statement Second pass ended appears in the message window Close Button Load Var Def Save Program Save Var Def begin defs dim s 512 1 Show Program end defs Show Var Def begin lists Ena phi x x x x e ph2 x x x x asgl a a a a OO sgl b b b b end lists Compile Validate begin exp SPT QUAD Abort sweep x 1 to sx R shot i 1 to h Validate p2 phi dx Button p0 ph2 a dl File Hepon f Selection i PuiseSPEL Programming Panel echo_ir exp edited dir lusripeopleirtwieprFilesiPuiseSPEL sharedPulse Edit Search Compile Properties Options echo detected inversion recovery acq sgl next i dx dx d30 next x Message Window pa Loaded file fusr people rtw xeprFiles Pulse SPEL sharedPulse SPEL Standard Pulse SPEL2000 SPEL2 echo_ir exp Figure 6 6 Validating the PulseSPEL program 9 Close the PulseSPEL window Double click the close button E 580 User s Manual 6 7 Inversion Recovery with Echo Detection p2 po p1 Acquisition Trigger 5 r NN gt d2 d1 d1 do ax j
131. ectrum E 580 User s Manual 4 5 Acquiring a FID with the Pulse Tables An Alternative Experiment 4 1 2 We acquired not only the FID but also the microwave pulse leak through and the deadtime in the previous section To avoid acquiring extraneous information we can adjust the Acquisition Trigger position to start data acquisition at the end of the dead time If you have completed Steps 1 7 of Section 4 1 1 proceed with the following steps 1 Adjust the Acquisition Trigger to start at the end of the dead time Edit the position for the Acquisition Trigger in the Patterns panel while observing the Spec Jet panel until the first data points of the FID after the deadtime are at the left hand edge of the SpecJet display See Figure 4 6 2 Press the Run button The spectrometer then acquires the FID and it appears in the viewport 3 Save the spectrum Record the Acquisition Trigger Position value in the spectrum title FI EPR Parameters Pattems l Feld l RF l Acquisition Scan Options 10 000 PULSE PATTERNS A p ml Channel Selection Acquisition Trigger zi Shot Rep Time us 999 60 z Integrator Time Base ns Single Point y Shots Per Point 1 e 5 000 hee Edit 7 Start position fw fs0 20 fo JoJo 5 000 Pos Disp ns fo _ Jo Length Inc ns gt Acquisi C j i 7 tion Trigger m re 0 500 1000 1500 2 000
132. ee Pulse ESEEM 17 Click the Hamming button in the Window Func tion task bar The Hamming window dialog box appears prWintamiming Slice current v all x Max C O x0 f0 App ly ee Function Clo se Button See Button Apply Close Herp Figure 6 36 The Hamming window dialog box 18 Click the Slices All button This ensures that the Hamming window is applied to each of the slices of our two dimensional dataset If you do not perform this step you will receive an unpleasant surprise Your 2D dataset is converted into a 1D dataset 19 Click the Apply button followed by the Close but ton The default values work well for this example 20 Transfer the Result dataset to the Primary dataset After you click Close a dialog box appears asking if you want to Move result to input Click Yes Please decide Move result to input Figure 6 37 Transferring the Result dataset to the Primary dataset E 580 User s Manual 6 37 Three Pulse ESEEM 21 Transformations f imagini Zero Filling ey prFFTic Fitting FFT prrFTepix Structure FFT Real Sice current all 2D FFT XSophe eeu type gt twa ProDeL Cross Term Averaging Automatic Convolition G ae Fae undo Deeenvelition Select the FFT command Click its button in the Transformations submenu of the Processing menu Diff
133. eed to estab lish an axis system or reference frame The reference frame which most people are familiar with is the lab frame which con sists of three stationary mutually perpendicular axes The lab frame in EPR is usually defined as in Figure 2 1 The magnetic field Bg is parallel to the z axis the microwave magnetic field B4 is parallel to the x axis and the y axis is orthogonal to the x and z axes All discussions of the electronic magnetization in this section will be described in this axis system Magnet Figure 2 1 Definition of the lab axis system When an electron spin is placed in a magnetic field a torque is exerted on the electron spin causing its magnetic moment to precess about the magnetic field just as a gyroscope precesses in a gravitational field The angular frequency of the precession is commonly called the Larmor frequency and it is related to the magnetic field by oL Y Bo 2 1 where is the Larmor frequency y is the constant of propor tionality called the gyromagnetic ratio and Bg is the magnetic W J A m a i Pulse EPR Theory field The sense of rotation and frequency depend on the value of y and Bo A free electron has a y 2n value of approximately 2 8 MHz Gauss resulting in a Larmor frequency of about 9 75 GHz at a field of 3480 Gauss The Larmor frequency corre sponds to the EPR frequency at that magnetic field Let us co
134. ent 00 F 1 BO CUUP EE dncinaaedecea anne sailed sonceadan cums kon eioueis takwnnadeaaiecuabseadecseaes F 1 BD Coarse NOPUSINICHL 2rpicct aot eetcctun andes nace aseceietesaccutoa a F 2 xii BRORER Ga Introduction 1 This document describes the operation of a Bruker Elexsys E 580 EPR Electron Paramagnetic Resonance spec trometer It is assumed that you have already read and mastered the material in the E 500 User s manual and that you are familiar with CW Continuous Wave EPR Many of the elementary principles necessary for following the chapters are presented in a concise form in Chapter 2 Using this Manual 1 1 How to Find Things 1 1 1 Preface Chapter 2 Chapter 3 Chapter 4 First you should read the safety guide in the preface of the man ual Microwaves can be dangerous particularly to your eyes With normal precautions the risk for injury can be minimized Users who are not familiar with Pulsed EPR should start by reading Chapter 2 which is a concise introduction to the theory and practice of Pulsed EPR spectroscopy It is by no means exhaustive it gives the necessary information to follow the other chapters of the manual A list of references is given at the end of the chapter for more information This chapter is a simple how to section describing how to pre pare for safe spectrometer operation It covers tuning the micro wave resonator and bridge switching to pulse mode and
135. ent in this chapter the FID There are two ways in which we can acquire data either through the pulse tables or through a PulseSPEL pulse program Each has its advantages The pulse tables are quick and easy but do not allow you to use any phase cycling The pulse program requires a few more steps but it does support phase cycling In the end most important data is acquired with a pulse program using phase cycling The pulse tables are usually used to quickly set up some preliminary experiments All these experiments use the DPPH sample that is supplied with the E 580 spectrometer It has a very simple spectrum consisting of one line of approximately 1 Gauss width For educational pur poses we will actually be performing more experiments in this chapter that you normally would These additional experiments help to illuminate the effects of the acquisition trigger delay spectrum phasing field offset and artefacts E 580 User s Manual Acquiring a FID with the Pulse Tables Acquiring a FID with the Pulse Tables The Basic Experiment 4 1 4 1 1 1 Follow the instructions of Chapter 3 Follow all of instructions until the end of Section 3 3 You should have a DPPH sample inserted into the resonator with a 16 ns ety x and 20 ns acquisition pulse e
136. es of the microwave pulses are changed in a prescribed fashion while the two quadrature detection channels are added subtracted and exchanged to achieve the desired net effect Imbalances in the quadrature detector can distort the Fourier transformed signal We assume that both detectors in Figure 2 48 have exactly the same gains the reference phases are 7 2 phase shifted from each other and there are no DC off sets This is very difficult to realize in practice The imbalance in phase and amplitude causes aliasing in which positive frequency signals start appearing at negative frequencies and vice versa The DC offsets appear as large features at zero frequency The four step phase cycle See Figure 2 65 suppresses all of these quadrature artefacts In the first step of the phase cycle we apply a x pulse and store the channel a signal as the real data and the channel b signal as the imaginary data Next we apply a x pulse causing our signals to changes sign Therefore we sub tract the second set of signals in order that our FID does not can cel but instead becomes twice as large This step of the phase cycle eliminates the zero frequency artefact because the DC off sets are unaffected by the phase of the microwaves therefore subtraction cancels it out E 580 User s Manual 2 63 Pulse EPR Practice detect a pulse y Figure 2 65 detect b x Lo X B Si channel a ch
137. esonator module to the probehead sup port E 580 User s Manual A 11 Installing the Resonator Installing the Resonator A 2 The following instructions describe the installation of a FlexLine resonator in an ER 4118CEF cryostat 1 Install the waveguide SMA transition on the microwave bridge Attach the transition onto the microwave output flange of the bridge Remember to use the waveguide gasket between the bridge and transition and that the gasket is in the correct orientation See Figure A 11 The four waveguide screws fasten the tran sition to the bridge The female SMA connector of the transition should point downwards Figure A 11 The right and wrong way to install the waveguide gasket 2 Place the resonator module probehead support through the NW50 o ring and its centering ring 3 Insert the resonator assembly through the top flange of the cryostat Make sure that the modulation Installing the Resonator and thermocouple connectors of the probehead support face towards the front See Figure A 12 e O ring and I centering ring Figure A 12 Inserting the resonator assembly through the o ring and into the cryostat 4 Clamp the resonator assembly firmly to the cry ostat Place the o ring clamp around the two o ring flanges and tighten by turning the wing nut See Figure A 13 Figure A 13 Tightening the o ring clamp with
138. ety Test Safety Test 3 3 The purpose of this section is to verify that everything is work ing and adjusted properly for safe operation 1 Verify that the HPP attenuator is set to 60 dB and the TWT is in standby mode See Figure 3 10 and Figure 3 2 2 Create a pulse experiment Click the Create New Experiment button Click the Pulse tab The Advanced button should already be active green If not click it Click the Create button Parameter Le x e m el aana Experiment Button iment Name Experiment Advanced Experiment Unit Goniometer J Gradient Unit Button ENDOR Calib Pulse sage A Advanced w FT EPR wv ESEEM wv HYSCORE wv Relaxation w ENDOR Create Cancel Help Figure 3 11 The Experiment dialog box E 580 User s Manual 3 9 Safety Test 3 Click the Activate button This ensures the parameter changes are immediately actuated by the spectrometer Activate Button Figure 3 12 The Activate button 4 Click the Parameters button See Figure 3 11 Set the magnetic field to a value at which there is no EPR signal Click the Field tab A Center Field of 2000 G and Sweep Width of 100 G is often a good value Figure 3 13 The Field parameter panel 3 10 fke Safety Test 6 Program a 16 ns x pulse Click on the Patterns tab Click the Channel Selection button and select x Click in the first Length box and enter 16 Figure 3 14 T
139. extension exp E 580 User s Manual D 31 PulseSpel Programming Panel ao Contents of this Group empty sharedPulseSPEL rtw s personal Pulse Spel programs Path tusripeopleirtwixeprFiles Pulse SPEL Create File show Filenames wa Cancel Help Figure D 11 The Load Program dialog box Save Program Saves the presently loaded PulseSPEL program Note that the standard Bruker PulseSPEL directories are write protected Save Program As Saves the presently loaded PulseSPEL program A dialog box appears allowing you to select a Path and Filename It func tions in a similar fashion to the Load Program dialog box Once you have selected the Path and Filename click Save Note that the standard Bruker PulseSPEL directories are write protected D 32 i PulseSpel Programming Panel New Variable Definitions Load Variable Definitions a Leesnet Contents of this Group empty sharedPulseSPEL rtw s personal PulseSpel programs Path usripeopleirtwixeprFiles PulseSPEL Create File 1 show Filenames Select a program to replace or type a new path filename swe Cancel Help Figure D 12 The Save Program As dialog box Clears the presently loaded PulseSPEL variable definitions Loads a new PulseSPEL variable definition file A dialog box appears allowing you to select a definition file One means of selecting a definition f
140. field See Beg ESEEM 2 37 three pulse 6 20 to 6 41 acquisition 6 29 to 6 33 processing 6 33 to 6 41 setup 6 21 to 6 29 two pulse acquisition 5 35 to 5 38 processing 5 38 to 5 44 excitation 2 43 to 2 44 external trigger C 14 to C 15 F FFT Also see Fourier theory FID 4 20 to 4 23 HYSCORE 7 19 three pulse ESEEM 6 38 Index two pulse ESEEM 5 42 FID acquisition 4 1 to 4 13 with pulse tables 4 2 to 4 7 with PulseSPEL 4 8 to 4 13 processing 4 14 to 4 27 field position C 8 sweep 2 52 to 2 54 sweep vs frequency spectrum 2 33 swept spectrum pulse tables 5 15 to 5 20 PulseSPEL 5 25 to 5 34 fitting exponential echo decay 5 24 5 38 to 5 39 inversion recovery 6 17 to 6 19 T 5 7 to 5 8 Fourier theory 2 21 to 2 32 convolution theorem 2 28 Fourier transform 2 24 pairs 2 24 to 2 25 properties 2 26 to 2 27 practical example 2 29 to 2 32 FS C 19 FT EPR parameters C 1 to C 22 acquisition panel C 10 to C 11 field panel C 8 to C 9 options panel C 14 to C 17 patterns panel C 2 to C 7 scan panel C 12 to C 13 accumulated scans C 13 all visible C 17 auto scaling C 12 averages per scan C 12 number of scans C 13 pattern control C 16 replace mode C 12 scans done C 13 G gaussian 2 24 getting started 3 1 to 3 24 gyromagnetic ratio 2 4 H hard pulse 2 40 holeburning 2 40 homogeneous broadening 2 19 how to use manual 1 1 to 1 3 HPP attenuator 2 44 3 7 HYSCORE 7 1 to 7 2
141. file D 31 to D 35 load program D 31 load variable definitions D 33 new program D 31 new variable definitions D 33 PulseSPEL path D 35 save program D 32 save program as D 32 save variable definitions D 34 save variable definitions as D 34 options D 41 properties D 40 to D 41 panel position D 41 show buttons D 41 search D 38 to D 39 replace string D 39 search selection backward D 39 search selection forward D 38 search string D 38 pulse tables vs PulseSPEL D 42 to D 44 reference manual D 1 to D 44 setting up experiment D 23 to D 28 structure D 4 to D 8 defs D 3 D 4 to D 5 exp D 7 to D 8 lists D 5 to D 7 validate D 25 variable definitions D 2 to D 4 variables D 3 to D 4 delay D 4 D 8 general D 3 increment D 4 pulse length D 4 D 8 rf D 4 spectrum size D 4 Q Qvalue 2 61 quadrature detection 2 45 to 2 46 artefact 4 22 artefacts 2 63 4 7 to 4 8 R Rabi frequency 2 8 real samples advice for 5 45 to 5 46 relaxation time 2 15 to 2 21 spin lattice 2 15 to 2 18 spin spin 2 21 transverse 2 19 to 2 21 resonator 2 61 to 2 62 exchanging resonator modules A 18 to A 23 gas flow A 17 installation of A 12 to A 14 microwave data A 25 module A 7 designation A 7 parts description A 2 to A 3 Index probehead support A 4 to A 6 sample holder A 8 to A 9 sample rod A 10 sample supports A 24 semi rigid coaxial cable A 11 tools A 11 user s guide A 1 to A 25 waveguide SMA transition A 11 ring down 2 61 3 18
142. fit through the hole at the same time The two wires are also of different length thread the shorter wire through the hole followed by the longer wire Make sure the white plastic bushing remains on the probehead support semi rigid cable 8 Carefully store the resonator module in a safe dry and clean place A 20 i Changing Resonator Modules Installing a Resonator Module A 4 2 l 2 Remove any module that is already installed Put the semi rigid cable of the support through its hole in the module mounting flange See Figure A 18 Make sure the white plastic bushing is still on the probehead support semi rigid cable Feed the modulation and thermocouple wires through the holes in the module mounting flange See Figure A 18 Note the two modulation connectors will not fit through the hole at the same time The two wires are also of different length thread the longer wire through the hole followed by the shorter wire Semi rigid Hole Modula tion Hole Figure A 18 Upper view of the module mounting flange 4 Attach the four 3x10 mm screws loosely You should be able to easily rotate the module See Figure A 17 E 580 User s Manual A 21 Changing Resonator Modules 5 Rotate the module so that the semi rigid cable lines up with the tube and the male and female SMA connectors line up See Figure A 19 Properly Aligned Crooked Figure A 19
143. fit an exponential curve to your echo decay The value Tau is the fitted T value it should be approxi mately 500 ns Processing Diff amp Integ Filtering Algebra Peak Analysis Complex Window Functions Transformations raging Fitting Structure XSophe ProDeL Automatic undo BN ARN ZN EN NN Gk A Polynomial Splines _ Line Shapes _ _Exponentials Saturation Curve Spectral Titration Define User Function Remave Ieor Function prfitExpDec Slice all current 1194 83 amplitude Tau Value fit amplitude yes VU no 442 89201 A yes v no Exponential Decay Command Tau fit Tau Help Biexponential Decay Arrhenius Figure 5 27 Fitting an exponential to the echo decay 5 24 i Field Sweeps with PulseSPEL Field Sweeps with PulseSPEL We already acquired an echo detected field swept EPR spectrum in Section 5 3 Here we shall acquire a field swept spectrum with a PulseSPEL program The pulse program allows us to per form a two step phase cycle The first pulse is alternated between x and x while the signals are alternately added and subtracted from the dataset This phase cycle serves two pur poses First the FID signal after the second pulse is independent of the first pulse s phase and therefore is canceled by the subtra tion The FID can cause diff
144. gram Normal y _aose_ PulseSPEL Help Figure C 9 The Acquisition panel Abscissa Quantities and Sizes X Axis Quantity Y Axis Quantity C 4 1 The quantity to be scanned for the x axis Clicking the arrow on the right hand side causes a drop down menu to appear For an E 580 spectrometer without pulsed ENDOR you can choose between Time and Magnetic Field The quantity to be scanned for the y axis of a two dimensional dataset It functions similarly to X Axis Quantity Note that both X Axis Quantity and Y Axis Quantity cannot both be simulta The Acquisition Panel neously Time or Magnetic Field if Y Axis Size gt 1 For a two dimensional time dataset you must use a PulseSPEL pro gram to acquire the dataset X Axis Size The number of points along the x axis of the dataset Y Axis Size The number of slices in a two dimensional dataset One indi cates a one dimensional dataset Acquisition Mode C 4 2 Run from Tables Run from PulseSPEL Read Transient Start Transient There are four options for the Acquisition Mode There is also a button to select quadrature detection The acquisition is controlled by what is programmed in the pulse tables The acquisition is controlled by a PulseSPEL program If you have an averaged signal already present in the SpecJet Display this mode will transfer that data into the Primary dataset of the active viewport when you click the
145. gt Figure 6 7 Variable definitions for the modified echo_ir exp 10 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 6 8 Set the variables to the values indi cated in Table 6 1 Variable Value d1 400 ns d2 96 ns do 0 ns d30 4 ns pO 16 ns p1 32 ns p2 32 ns h 10 A Table 6 1 Variable values for the setup experiment Inversion Recovery with Echo Detection FT EPR Parameters Patterns ABSCISSA QUANTITIES AND SIZES RF Acquisition l Scan l Options l X Axis Quantity Time x X Axis Size 512 Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables P 4 Run from PulseSPEL Coremans PulseSPEL Read Transient Variable Start Transient B Ox PulseSPEL ACQUISITION PulseSPEL Program SPEL2 fidcycle_bestep exp PulseSPEL Variable d0 40 ns Experiment EXP y Phase Cycling LISTS y Phase Program Normal y PulseSPEL Help Figure 6 8 Editing PulseSPEL variables 11 12 13 Increase the HPP attenuator by 1 dB We optimized the microwave power for two 27 3 pulses in Section 5 2 Here we need the 16 ns pulse to be a 7 2 pulse Press the Run button The spectrometer then acquires the inverted echo and it appears in the viewport This pulse program will go through the four steps of the phase
146. he Patterns panel E 580 User s Manual 3 11 Safety Test 7 Program a 20 ns Acquisition Trigger Click the Channel Selection button and select Acquisition Trig ger Click in the first Length box and enter 20 See Figure 3 14 8 Open the SpecJet window Click the SpecJet button SpecJet Display SpecJet Button mr E EL 0 500 1 000 1500 2 000 i Timefns AVERAGING TIME BASE Time Base ns 40 No Settings Button Stop k Qose Settings Help No of Averages 100 Averages Done 0 Figure 3 15 The SpecJet window Safety Test 9 Open the SpecJet Settings window Click the Set tings button to open it Figure 3 16 The SpecJet Settings window 10 Set some SpecJet parameters Set the No of Aver ages to 100 Set the No of Points to 512 Set the Time Base to 4 ns Click the Repetitive Mode button to acti vate it green button Make sure both Channels and 2 are activated green E 580 User s Manual 3 13 Safety Test 11 Click the Run button in the SpecJet window This activates the SpecJet to acquire data 100 Figure 3 17 The Run button Run Button 512 3 14 shg Safety Test 12 Click the Start button in the Patterns panel This starts the pulse programmer Figure 3 18 The Start button E 580 User s Manual 3 15 Safety
147. he SpecJet In integrator mode the integrator gate width is determined by the parameter pg The command is followed by a sign program identifier that refers to a sign pro gram defined in the definition section of the program acq SG1 Note that there is no a or b preceding the identifier it is the final number 1 that identifies the sign program The digitizer command initiates a transient recorder measure ment by the SpecJet The command is followed by a sign pro gram identifier that refers to a sign program defined in the definition section of the program dig SG1 Note that there is no a or b preceding the identifier it is the final number 1 that identifies the sign program PulseSPEL offers the operations of addition subtraction multi plication and division The following are all valid statements DO 88 D1 D2 5 D2 D1 Pl A 6 Z A B F DO A This is not valid statements pl pl p2 pod E 580 User s Manual The PulseSPEL Programming Language Shot Loops It is highly recom mended not to use the reserved vari ables X and y for Shot loop counters or limits These vari ables are used in other types of loops Sweep Loops It is not possible to use parentheses or multiple operations in algebraic expression You can overcome this by simplifying the mathematical expression and splitting into more than one state ment If you need to perform an operation such as pl p3
148. he Vali date button The pulse program is not only compiled but also each step is checked to verify that it is within the lim its of the spectrometer capabilities If successful the state ment Second pass ended appears in the message window PulseSPEL Programming Panel fidcycle_bestep exp edited dir lusripeopleirtwixeprFiles PulseSP EL Ishare File Edit Search Compile Properties Options Close Button Save Program FID detection with transient recorder using CYCLOPS off resonance baseline correction Save Var Def Show Program begin defs Show Var Def dim s 512 1 end defs begin lists phl x x y y Verbose On Off asgl a a b b on resonance sign program Compile bsgl b b a ta Validate asg2 a a b b off resonance sign program bsg2 b b a a Abort end lists Validate begin exp quad trans Button shot i 1 to 2 pO ph1 dao dig sg1 next i bestep 200 ff resonance step Message shot i 1 to 2 pO ph1 Window do _ gt Second pass ended Help On Selection N Figure 4 11 Validating the PulseSPEL program 8 Close the PulseSPEL window Double click the close button E 580 User s Manual 4 11 Acquiring a FID with PulseSPEL 9 Press the Run button The spectrometer then acquires the FID and it appears in the viewport This pulse program will go through the fo
149. he spectrometer then acquires the inversion recovery and it appears in the viewport Run Button Figure 5 5 The Run button 12 Store the spectrum 13 Phase the data The real data should be an exponential recovery See Figure 5 6 and the imaginary data should be flat If you followed the directions in Section 4 1 cor rectly phasing should not be necessary If there is an appreciable amount of the inversion recovery signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat SSS SSS 0 200 400 600 800 000 4200 1400 1600 1800 2000 Time ns Figure 5 6 Inversion Recovery of DPPH Inversion Recovery with FID Detection 14 Multiply the spectrum by 1 Click the Constant Operation command in the Algebra submenu of the Pro cessing menu The Constant Operation dialog box appears Enter 1 in the Val window and click the mul tiply button Click the Apply button followed by the Close button Processing imagini Primary Secomiary Fitting Peary Secontlary Structure XSophe Constant Operation Diff amp Integ Command Filtering Algebra R Peak Analysis Constant Operation i Complex ordinate Multiply Window Functions Pt nery Secendary Transformations Pamery Secondary prCstOperation Button
150. ibes how to turn the Bruker E 580 spectrome ter on and prepare for safe operation Many of the procedures are described in detail in the Bruker E 500 User s Manual in Section 3 1 It also explains how to change samples and turn off the spectrometer when you are finished To help you in the follow ing sections Figure 3 1 assists you in identifying the various units which comprise the EPR spectrometer y Bridge TWT Bridge Controller pn Field Controller _ Digitizer qe Acquisition Server Pulse Programmer Resonator Power Magnet Supply Figure 3 1 The modules and components of the Elexsys E 580 spectrometer E 580 User s Manual Turning the Spectrometer On Turning the Spectrometer On 3 1 l Follow the instructions in Section 3 1 of the Bruker E 500 User s Manual Consult the E 500 User s Manual for instructions on powering up the con sole turning on the magnet power supply and water log ging in to the workstation and connecting to the spectrometer Turn on the TWT Press the power switch After a five minute warm up period it will wake up in Standby mode Continue with the rest of the instructions while it is warm ing up Power Switch Power Standby Indicator Figure 3 2 The power switch fo
151. ices The digitizer captures and averages the FID and echo signals The Pulse EPR Bridge 2 2 1 The microwave bridge creates the microwave pulses and detects the FIDs and echoes Because of this two fold duty for the pulse bridge it is a good idea to separate the two functions in our dis cussions A few of the parts are actually required for both excita tion and detection Detection cw Quadrature Detection Detection A CW Channel Microwave Low Power Oscillator Pr Pulse Channel Circulator Pulse Channels Amplifier Probehead Excitation High Power pii High Power Figure 2 44 A block diagram of the bridge separated into its two functions 2 42 Pulse EPR Practice Excitation In order to excite or produce an FID or echo we need to create a short high power microwave pulse Typical pulse lengths are 12 16 ns for a 7 2 pulse with up to 1 kW of microwave power This is achieved by supplying low power microwave pulses to the TWT where they are amplified to very high power See Figure 2 45 The MPFU Microwave Pulse Forming Unit produces the low power microwave pulses Each unit consists of two arms with individual attenuators and phase shifters to adjust the relative amplitudes and phases in the two arms To create a x pulse the x PIN P type Intrinsic N type diode switch passes micro waves through for the specified pulse length For
152. iculties particularly if both narrow and broad signals are simultaneously present Any offsets are also independent of the first pulse s phase and also are cancelled X X pe B l u X WW Figure 5 28 Two step phase cycle 5 5 In this section we shall once more reinforce the idea of perform ing a setup experiment first to determine the timing field and power followed by the experiment we ultimately want to per form E 580 User s Manual 5 25 Field Sweeps with PulseSPEL The Two Pulse Echo Setup Experiment 5 5 1 l Follow the instructions of Section 5 2 Follow the steps up to and including Step 13 Activate PulseSPEL Click the Run from PulseSPEL button in the Acquisition panel FT EPR Parameters ABSCISSA QUANTITIES AND SIZES Pattems Field RF Acquisition l Scan l Options l X Axis Quantity Time y X Axis Size 1024 m Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables Quadrature Detection E Run from PulseSPEL v Transient y Starts soa aa Run from PulsesPEL Po PulseSPEL Exper Button a ees PulseSPEL y Button x Cose PulseSPEL Help Figure 5 29 The Run from PulseSPEL button 5 26 Field Sweeps with PulseSPEL 3 Launch the PulseSPEL window Click the Puls eSPEL button and the PulseSPEL window appears See Fig
153. ide of the table are labels identifying the rows Indicates the time resolution used for the channel The PatternJet allows either 4 or 2 ns resolution Identifies which PatternJet board is used to control the channel The leftmost board is Board 1 and board numbers increase towards the right Identifies the connector on the PatternJet board used to control the channel 2 ns Mode 4 ns Mode Figure E 3 Connector locations The delay used to automatically calculate the timing of the indi vidual channels to safely and correctly perform a pulse experi ment The extra pulselength required to automatically calculate the timing of the individual channels to safely and correctly perform a pulse experiment E 580 User s Manual Options Options E 3 OPTIONS Figure E 4 The Options panel Single Point Selects either the SpecJet or SDI Sampling Digitizer as the sin Recorder Type gle point digitizer Older systems may still have an SDI board E 6 BRORER Options Field Modulation Turns off field modulation when active It is active when green E 580 User s Manual E 7 Notes sD BROKER EPL Phase amp Amplitude Adjustment F This appendix describes the procedure for adjusting the phases and amplitudes of the X X Y and Y microwave pulse chan nels The first part of the adjustment looks solely at the TM Transmitter Monitor signal whereas the second
154. ii ni an a a O E aE C 11 Co The Scan Panel oenen a e a a O triscesalaSiueuses C 12 C6 The Options Pane bss scssisschabseavishattiasiviaine tack dinette C 14 C 6 1 Acquisition Tig gers cscs cuvissdeteanedtceuctatacactaasesateaaeassreeetaavaesanonsdeacbeassies C 14 C 6 2 Pulse Patternsivn cian cestdevcices E a a E EE C 16 C7 The SpecJ et Display snes sszctsesdSstactseesss terete cadoeaie iaaa C 18 xX BRUKER Table of Contents Gi AVCPA SIN Gidea decides A Rae a aoe decks saad cae ea eee C 19 C72 TIME Base secs at i Minden tea Sheed na a aa e e Se O oda sed aa ts tana eete bess C 19 Gi7 3 Speclet Sewn evickssivazs mee iea ee n a OE EEA Bacau abeeds C 20 GTA AVera CME 23 508 n a E a a A bes C 21 COTS Time Basena a week E aae a a E E lites vewsiees C 21 AA A TMS BOF E A E EE EE E A d ctedavecdeaeiubutestevesevess C 22 Appendix D PulseSPEL Reference Manual 05 D 1 D 1 The PulseSPEL Programming Language cccccceeseceteeeeeenteeeteeeees D 2 Di lel Variable Definitions suiriri oe eave i E D 2 D 1 2 The Structure of PulseSPEL Programs ccccecsseesseeseceneesteeeeeeeteeeeeeses D 4 D 1 3 Commands and Operations cccccccseesseesseeseceeeceeeeeeeeeeeecaeeesecnseeneeneeesss D 8 DV A An Example n naa svi loczevagnedies soecanevansasiiets a E aA D 14 D 1 5 Multi Section PulseSPEL Programs ccceccccsseesecetceeseceeeeeeeeeeeseeensees D 16 D 2 The PulseSPEL Acquisition Panel 00 0 0 c
155. il the imaginary trace is flat z R 3 o 200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 2000000 Time ns Figure 6 14 The inversion recovery of a coal sample 13 Multiply the spectrum by 1 Click the Constant Operation command in the Algebra submenu of the Pro cessing menu The Constant Operation dialog box appears Enter 1 in the Val window and click the mul tiply button Click the Apply button followed by the Close button W J A m a i Inversion Recovery with Echo Detection Processing Diff amp Integ a Filtering Algebra AA Peak Analysis a Constant Operation Complex _ ordinate Window Functions Primary Secondary Transformations PSntry Secondary imagi Primary Secomiary Fitting PENRY Seconlary Structure r XSophe ProDeL Constant Operation Command Multiply prCstOperation Button Slice v current P Operation vi vily C Automatic Value Window Jom w Figure 6 15 Multiplying the spectrum by 1 14 15 dataset Transfer the Result dataset to the Primary Fit a decaying exponential to measure T4 Click the Exponential Decay command in the Exponentials submenu of the Fitting subnenu The Exponential Decay dialog box appears Click the Fit button and the program will fit an exponential
156. ile is to navigate to the desired path in the Group box and double click the definition filename in the Con tents of this Group box Another method is to type the path and definition filename into the Path and File boxes and then click Load Definition files have the three letter extension def The standard Bruker variable definition file is descr def E 580 User s Manual D 33 PulseSpel Programming Panel Save Variable Definitions Save Variable Definitions As agPgDefloat i is sr a ae Contents of this Group empty sharedPulseS PEL Path tusripeopleirtwixeprFiles PulseSPEL Create File J _1 show Filenames Load Cancel w Figure D 13 The Load Variable Definitions dialog box Saves the present variable definitions Note that the standard Bruker PulseSPEL directories are write protected Saves the presently loaded variable definitions A dialog box appears allowing you to select a Path and Filename It func tions in a similar fashion to the Load Program dialog box Once you have selected the Path and Filename click Save Note that the standard Bruker PulseSPEL directories are write protected D 34 PulseSpel Programming Panel PulseSPEL Path VA J gt K In order for this change to be perma nent remember to save changes when you exit the Xepr program Contents of this empty sharedPulseSPEL Path
157. imensional ESEEM experiment It is essentially a three pulse ESEEM experiment with a m pulse between the sec ond and third pulses Nia NIA a Nia Figure 7 1 The HYSCORE experiment We shall use the Bruker supplied coal sample for the experi ment A four step phase cycle is required to remove unwanted echoes so we shall use PulseSPEL to acquire the data A ces af X X B i i X X A B C D C l X X D oa X X Figure 7 2 The four step phase cycle for the last two pulses of a HYSCORE experi ment E 580 User s Manual The HYSCORE Setup Experiment The HYSCORE Setup Experiment 7 1 l Follow the instructions of Section 5 2 Follow the steps up to and including Step 13 Activate PulseSPEL Click the Run from PulseSPEL button in the Acquisition panel FT EPR Parameters ABSCISSA QUANTITIES AND SIZES Pattems Field RF Acquisition l Scan Options X Axis Quantity Time y X Axis Size 1024 Y Axis Quantity Magnetic Field x Y Axis Size 1 z ACQUISITION MODE v Transient v Si a Run from PusesPeL Prod PulseSPEL Experi Button 7 Puses PulseSPEL Phase Cytmng Button y v Run from Tables Quadrature Detection Run from PulseSPEL Lt Close PulseSPEL Help Figure 7 3 The Run from PulseSPEL button The HYSCORE Setup Experiment Launch the PulseSPEL window Click the Pul
158. iment 2 18 i Pulse EPR Theory Transverse Relaxation Time The transverse relaxation time corresponds to the time required for the magnetization to decay in the x y plane There are two main contributions to this process and they are related to differ ent broadening mechanisms homogeneous and inhomogeneous broadening Figure 2 17 a Homogeneous broadening The lineshape is determined by the relaxation times and therefore lorentzian lineshapes are a common result See Equation 2 13 and Figure 2 21 The EPR spectrum is the sum of a large number of lines each having the same Larmor frequency and lin ewidth b Inhomogeneous broadening The lineshape is determined by unresolved couplings because the EPR spectrum is the sum of a large number of narrower individual homogeneously broadened lines that are each shifted in frequency with respect to each other Gaussian lineshapes are a common result E 580 User s Manual 2 19 Pulse EPR Theory A spin packet is one of the many individ ual homogeneously broadened EPR lines that contributes to an inhomogeneously broadened EPR spectrum See Figure 2 17 a a In an inhomogeneously broadened spectrum the spectrum is broadened because the spins experience different magnetic fields These different fields may arise from unresolved hyper fine structure in which there are so many overlapping lines that the spectrum appears
159. in Section 5 2 cor rectly phasing should not be necessary If there is an appreciable amount of the decaying exponential signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat Extract the real part of the dataset Once properly phased only the real part of the dataset contains the infor mation we seek Click the Real Part command of the Complex submenu of the Processing menu Processing Diff amp Integ Filtering z Algebra 3 Real Part Peak Analysis magus Command Window Functions Absolute Transformations Power Braginy Real Part Imag Part Re lt gt m Conjugate Budd Canptex Fitting Structure XSophe ProDeL Automatic Figure 5 41 The Real Part command 11 Fit a decaying exponential to the echo decay Click the Exponential Decay command in the Expo nentials submenu of the Fitting subnenu The Exponen tial Decay dialog box appears Click the Fit button and the program will fit an exponential curve to your echo decay Click the Close button to close the dialog box 5 38 Two Pulse ESEEM Processing prFitExpDec Diff amp Integ Slice current v all Filtering Fei F amplitude 1194 83 Tau Value nsn en fit amplitude yes no Complex Window Functio
160. in the viewport This pulse pro gram will go through the two steps of the phase cycle Save the spectrum Find where echo begins and ends Place your cur sor on the spectrum and determine from the readout at what time the top of the echo occurs See Figure 5 16 Record this number somewhere Determine the width of the echo and record it somewhere E 580 User s Manual 5 31 Field Sweeps with PulseSPEL The Echo Detected Field Sweep 5 5 2 l Follow the instructions of Section 5 5 1 We are using that experiment as the setup experiment for the present experiment Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file echo_fs exp and click the Load button agPgload Group Contents of this Group 2Dfidinvrec 2Dstd 2Dstd_av 2Dstd_set 2p_eseem 4pulse_eseem 4pulse_eseem2d echo2phi echo_ir fi PulseSPEL Program Path aredPulseSPEL Standard Pulse SPEL2000 SPELZ Greate File echo_fs exp show Filenames fo Cancel Help Load Button Figure 5 35 Selecting the PulseSPEL program 3 Validate the PulseSPEL program Click the Vali date button The pulse program is not only compiled but also each step is checked to verify that it is within the lim its of the spectrometer capabilities If successful the state
161. intense microwave pulse analogous to a hammer strike and digitize the signals coming from the sample After Fourier transformation we obtain our EPR spectrum in the frequency domain EPR has traditionally been a CW Continuous Wave spectros copy The NMR spectroscopist enjoyed substantial gains in sen sitivity with a correspondingly drastic reduction in measurement time by moving to a pulse FT technique because they have a large number of very narrow lines spread over a wide compared to the linewidth frequency range In most cases the EPR spec E 580 User s Manual troscopist is unable to enjoy these sensitivity improvements because EPR spectra are usually broad and not as numerous Why would EPR spectroscopists wish to switch to a pulse meth odology without the promise of increased sensitivity NMR spectroscopists soon discovered by measuring in the time domain and using multi dimensional techniques they were able to extract much more information than they ever could possibly imagine We can enjoy these same advantages in EPR as well Perhaps one of the most common pulse EPR applications is ESEEM Electron Spin Echo Envelope Modulation in which you obtain information regarding interactions of the electron spin with the surrounding nuclei Interpretation of the data yields important structural information particularly for large metallo proteins for which no single crystals are available for X ray dif fraction and the mole
162. inuously average The SpecJet repeatedly averages the signal and then updates the display with the aver aged signal This mode is very useful for setting experiments up See Section 3 3 C 7 5 The time resolution of the acquisition The number of points to be acquired It can range from 32 to 4096 points It must be an integral power of two Time Base x No of Points The SpecJet should always be run with the external clock so that the PatternJet and SpecJet are synchronized Should the SpecJet find itself in an undefined state the Reset button resets the SpecJet E 580 User s Manual C 21 The SpecJet Display Trigger Trigger Mode Trigger Source Trigger Slope Trigger Level C 7 6 The SpecJet can operate as an oscilloscope Therefore it has many of the same trigger features of an oscilloscope Figure C 16 The SpecJet trigger connections Not implemented yet The SpecJet can trigger from either one of the input signals Int Ch1 or Int Ch2 It normally triggers from an ECL trigger from the PatternJet pulse programmer Ext ECL Ext TTL allows you to trigger the SpecJet with an external TTL pulse Selects whether the SpecJet triggers on a rising or falling edge Adjusts the voltages level needed to trigger the SpecJet C 22 W J A m a PulseSPEL Reference Manual D PulseSPEL Pulse SPEctroscopy Language is a compiled pro gramming la
163. ired channel and the timing values for that channel are displayed in the pulse tables The first channel is the Acqui sition Trigger for triggering the SpecJet digitizer or whatever acquisition device has been specified in the spectrometer config uration The next items in the list are the different microwave pulse channels If you have pulsed ENDOR RF gates will also appear Figure C 2 Channel Selection Start amp Stop The Start button starts a pulse sequence produced by the Pat ternJet pulse programmer The Stop button stops the pulse sequence E 580 User s Manual C 3 The Patterns Panel Edit Commands Position Length C 2 1 To edit pulse table variables you must first select the channel you wish to edit with the channel selector Each channel can have up to 32 separate pulses Each pulse is characterized by four parameters defined in Figure C 3 Pos Disp and Length Inc are the step sizes for changing the position and length respectively H Pos Disp Length Inc Figure C 3 Definitions of the four pulse parameters If the PatternJet channel is operating in 4 ns mode values will increase and decrease in steps of 4 ns Click the entry in the pulse tables to edit it The box will be high lighted and two arrows will appear on the right hand side Click ing the up arrow increasing the value by 2 ns and the down decreases the value by 2 ns When the lt Ctrl gt
164. is an introduction to the basic theory and practice of Pulse EPR spectroscopy It gives you sufficient background to understand the following chapters In addition we strongly encourage the new user to explore some of the texts and articles at the end of this chapter You can then fully benefit from your particular pulse EPR application or think of new ones A common analogy for describing CW Continuous Wave and FT Fourier Transform techniques is in terms of tuning a bell We are assigned the task of measuring the frequency spectrum of the bell In one scheme for tuning the bell we use a frequency generator and amplifier to drive the bell at one specific fre quency In order to obtain a frequency spectrum of the bell we slowly sweep the frequency in order to detect any acoustic reso nances in the bell We essentially perform a similar experiment in CW EPR the field is slowly swept and we detect any reso nances in the sample This does not seem like the best means for tuning because we know from everyday experience that if we strike a bell with a hammer it will ring i e resonate acoustically at multiple frequencies So an alternative approach is to strike the bell digitize the resultant sound and Fourier transform the digitized signal to obtain a frequency spectrum Only one short experiment is required to obtain the frequency spectrum of the bell This fact is often called the multiplex advantage In FT EPR we apply a short but very
165. is defined relative to the last event the leading edge of the second microwave pulse i e d1 dx d0 z n 2 T l l le gt l lt gt d1 dx i d1 dx d0 l l I l l l l Second Acquisition Pulse Trigger Position Position Figure D 28 PulseSPEL timing The acquisition trigger still occurs at 2d1 2dx d0 after the lead ing edge of the first microwave pulse The difference is that the PulseSPEL program then constructs a time axis with a step size of dx 8 ns We have measured precisely the same echo decay with the same time resolution but now it appears that the echo is decaying twice as quickly We must therefore multiply any T value measured in a PulseSPEL experiment by two In an ESEEM experiment the situation is reversed The deter mining factor in this experiment is not the time after the first microwave pulse but the time between the two microwave pulse dl dx which is increment in 8 ns steps With the pulse E 580 User s Manual D 43 Pulse Tables vs PulseSPEL table experiment the step size is twice this value and therefore all the frequencies in the Fourier transformed spectrum must be multiplied by two in a pulse table experiment D 44 akGien Configuration Table E The Spectrometer Configuration window has a panel specifi cally for the FT EPR configuration The configuration window is launched by clicking the Spectrometer Configuration com m
166. is the m pulse is twice as long as the 7 2 pulse and therefore will limit the amount of the EPR spectrum we can excite See Figure 2 21e With a bit of calculus it can be shown that the maximum echo height for two equal length pulses is achieved with two 27 3 120 pulses See Figure 2 41 The narrower 27 3 pulses excite a broader portion of our spectrum than the z pulse can F i Na T N ald a 1 nfe Figure 2 41 Simulated echo shapes for different tip angles E 580 User s Manual 2 39 Pulse EPR Theory y Holeburning means to excite a narrow frequency range of an EPR spectrum The resultant reduced M leads to less detected EPR intensity in that nar row range thereby creating a hole in the spectrum Sometimes both hard short and soft long pulses are combined together in one experiment For example to perform a Davies pulse ENDOR experiment you use a soft n pulse to burn a nar row hole in the EPR spectrum See Figure 2 42 and two nar row pulses to detect it The resulting echo can be a bit puzzling at first glance It is actu ally the sum of two echoes one is a narrow positive going echo from the broad EPR spectrum and the other is a broad negative going echo from the narrow hole In order to adjust the z pulse the microwave power is varied until the area of the broad nega tive going echo is as negative as possible EPR Spectrum Lo Figure 2 42 Echo shapes in
167. ith experi mental options The outer most loop is the for next loop with k as its loop vari able This loop will be repeated n times Scansdone and totscans will inform us how much of the experiment has already been finished The next loop is the sweep loop It will increment the variable dx in steps of d30 in order to digitize the echo The innermost loop is the shot loop It performs the experiment shown in Figure D 1 It will be repeated h times Acquisition po p1 k Trigger oo d1 d1 do dx Figure D 1 Definition of the variables for echo2phi exp Both pO and acq have phase or sign programs The first time the sweep loop runs the first pulse is a X pulse and the results are added to the previous results The sweep loop will then run a second time with the first pulse being a X pulse and the results subtracted from the previous results The total number of averages in this example is n x h x number of phase cycle steps E 580 User s Manual D 15 The PulseSPEL Programming Language Multi Section PulseSPEL Programs D 1 5 Lists Sections Exp Sections Defs Sections So far we have considered only a single defs lists and exp section in our PulseSPEL program It is possible however to have multiple defs lists and exp sections in a single program Using multiple lists sections allows us to choose between sev eral different phase cycles without recompiling the PulseSPEL program Grouping several
168. key is pressed simultaneously while clicking an arrow the parameter changes in 20 ns steps When the lt Shift gt key is pressed simultaneously while clicking an arrow the parameter changes in 200 ns steps You can also click the entry a second time to enter a new value through the keyboard A cursor appears which can be moved to the desired position with the mouse or the left and right arrow keys Position ns C Oe Length ns hm 0 Pos Disp ns a ae Length Inc ns fo p Figure C 4 Pulse table entries i The Patterns Panel There is also a drop down menu with further editing functions Figure C 5 The Edit commands Select All Deselect All Copy Channel Cut Channel Paste Channel Selects all the entries in the present channel Deselects all the entries in the present channel Copies all the entries in the present channel Cuts all the entries in the present channel Pastes all the entries in the channel from which you cut or cop ied into the present channel E 580 User s Manual The Patterns Panel Cleanup Channel Clear Column Insert Column Delete Column Repeat Group Deletes any pulses of zero length and contracts the pulse pattern Clears all the entries sets all the values to zero in the presently active column A column is active when you have highlighted one of the column entries Inserts a new column before the presently active column Deletes the present
169. knobs to 0 0 F 2 Follow the instructions of Section 3 1 and Section 3 2 Use the Bruker supplied coal sample as your sample Create an Advanced pulse experiment Program a 20 ns Acquisition Trigger pulse at 0 ns in the pulse tables Program a 100 ns X pulse at 0 ns Program a 100 ns X pulse at 200 ns Program a 100 ns Y pulse at 400 ns Program a 100 ns Y pulse at 600 ns Open the SpecJet display window Activate Repetitive Mode on the SpecJet Phase amp Amplitude Adjustment 10 Deactivate Channel 2 11 Click the Start button of the pulse tables You will see a SpecJet display that qualitatively resembles the fig ure below 10 000 5 000 5 000 10 000 ya ot 0 500 1 000 1 500 2 00 0 Time ns Figure F 2 The four microwave pulses detected with the transmitter monitor 12 Click the 2 button in the SpecJet display win dow This magnifies the display by a factor of two E 580 User s Manual F 3 Phase amp Amplitude Adjustment 13 Adjust Monitor 1 also known as the TM phase knob until the X first pulse is maximized and positive Figure F 3 Maximizing the X pulse with the TM phase Phase amp Amplitude Adjustment 14 Adjust the phase knobs of X Y and Y until they are all maximum and positive Figure F 4 Maximizing the pulses by adjusting their indi vidual phases E 580 User s Manual F 5 Phase amp A
170. lated echo intact but subtracts the other echoes away See Figure 2 67 Almost all pulse EPR experiments are performed with some type of phase cycling in order to focus on the one echo or FID in which we are interested A x X X B X X X nla A B C D C p X X X D X X X m Nir Figure 2 67 Cancellation of unwanted echoes by phase cycling 2 66 Bibliography Bibliography NMR 2 3 This chapter is a brief overview of the basic theory and practice of pulse EPR spectroscopy If you would like to learn more there are many good books and articles that have been written on these subjects We recommend the following 2 3 1 The Principles of Nuclear Magnetic Resonance A Abragam Oxford at the Clarendon Press 1978 Principles of Nuclear Magnetic Resonance in One and Two Dimensions R R Ernst G Bodenhausen and A Wokaun Oxford Science Publications 1987 A Handbook of Nuclear Magnetic Resonance R Freeman Longman Scientific amp Technical 1987 Two Dimensional Nuclear Magnetic Resonance in Liquids A Bax Delft University Press 1982 Principles of High Resolution NMR in Solids M Mehring Springer Verlag1983 Experimental Pulse NMR A Nuts and Bolts Approach E Fukushima and S B W Roeder Addison Wesley 1981 E 580 User s Manual 2 67 Bibliography EPR Pulsed Magnetic Resonance NMR ESR and Optics D M S Bagguley Ed Oxford Scienc
171. lating at the microwave frequency See the upper series of Figure 2 3 An alternative way of looking at linearly polarized microwaves which is more useful when using the rotating frame is shown in the lower series of Figure 2 3 The sum of two magnetic fields rotating in opposite directions at the microwave frequency will produce a field equivalent to the lin early polarized microwaves As we shall see only one of the rotating components is important in describing the FT EPR experiment Figure 2 3 Linearly polarized microwaves represented as two circularly polarized components Alas the effect that B4 has on the magnetization is very difficult to envision when everything is moving simultaneously as in the first picture in Figure 2 4 To avoid vertigo we can observe what is happening from a rotating coordinate system in which W J A m a i Pulse EPR Theory we rotate synchronously with one of the rotating By compo nents We shall assume that we are at resonance i e oL 0 2 2 where o is the microwave frequency By rotating the coordinate system at an angular velocity of o we can make one of the components of B to appear stationary See second picture of Figure 2 4 The other component will appear to be rotating at an angular velocity of 2m and can be neglected The reasons for neglecting the fast component is based on effective fields and will be covered later in this ch
172. layed insert an empty sam ple rod into the reso nator to prevent air entry 10 11 13 Wait until you have a slight overpressure Monitor the pressure gauge on the flow controller Wait at least ten seconds after the gauge indicates one atmosphere of pres sure A handy indicator that works most of the time is the nitrogen flowmeter float it will pop up briefly if there is enough pressure Loosen the collet nut in the sample access area Quickly remove the sample from the resonator If you move too slowly the o ring in the sample access area may freeze Avoid contact with the cold objects to prevent frostbite Put the sample and sample rod in a safe place Get the new sample you prepared in Step 2 Pull the stopper out of the top of the sample rod Slowly insert the sample Take about five seconds to fully insert the sample Some gas may exit through the hole in the top of sample rod This gas flow purges the air out of the sample rod Reinsert the stopper in the top of the sample rod If the stopper fits loosely tighten the nut to ensure leak free operation Tighten the collet nut of the sample access area Turn the diaphragm pump on Wait for your sample to come to thermal equilib rium Even though your temperature controller indicates a low temperature it may require up to 15 minutes for your sample to cool down fully If you have run the last sample of the day and are shutting down remove your sa
173. le The preceding commands only change the display scaling not the actual data Starts a SpecJet acquisition Stops a SpecJet acquisition Closes the SpecJet Display window Activates the SpecJet Settings window See Section C 7 3 C 7 1 The number of acquisitions to be averaged The number of acquisitions that have been averaged C 7 2 The time resolution of the acquisition The number of points to be acquired It can range from 32 to 4096 points It must be an integral power of two E 580 User s Manual The SpecJet Display SpecJet Settings C 7 3 The remaining items are all elements of the SpecJet Settings window Figure C 15 The SpecJet Settings window Close Closes the SpecJet Settings window C 20 BRORER The SpecJet Display Averaging Channel 1 amp 2 Channel 1 amp 2 Offset Dither Mode No of Averages Averages Done Repetitive Mode Time Base Time Base No of Points Scan Time Clock Source Reset C 7 4 Allows you to select which SpecJet channels are acquired Green indicates the channel is active Both channels are required for Quadrature Detection Changes the DC offset of the incoming signals This is particu larly useful to separate the two traces for better visibility The offset does change the acquired data Not implemented The number of acquisitions to be averaged The number of acquisitions that have been averaged Allows you to cont
174. le A 4 1 1 Raise the coupling adjustment for easy access to the male SMA connector See Figure A 15 2 Detach the modulation wires from the modula tion pins See Figure A 15 Coupling Adjustment Modulation X Wires Thermocouple Figure A 15 Accessing the SMA connector Changing Resonator Modules Mounting Flange Free the modulation wires up to the mounting flange Rotate the cable restraints until the slots line up with the wires and then move the wires away See Figure A 16 Free the thermocouple wires up to the mounting flange Rotate the cable restraints until the slots line up with the wires and then move the wires away See Figure A 16 Cable Restraints Figure A 16 Freeing the wires 5 Loosen the male SMA connector with the 8 mm wrench Prevent the female SMA connector from mov ing with the 1 4 inch wrench The inner structure of the module is spring loaded and the connectors will spring apart E 580 User s Manual A 19 Changing Resonator Modules 6 Remove the four 3x10 mm screws from the mounting flange with the 2 5 mm Allen wrench See Figure A 17 3x10 mm Screw BS i Figure A 17 Removing the 3x10 mm screws 7 Carefully pull the resonator module away While removing the module thread the modulation and thermo couple wires carefully through the holes in the mounting flange Note the two modulation connectors will not
175. left shift is required The 10 G offset causes the signal to appear at 10 x 2 8 MHz 28 MHz or 0 028 GHz in the display Notice the artefact due to quadrature detection imbalances Also notice the admixture of absorption and dispersion O 0049999 0 099999 GHz Figure 4 28 FFT of Section 4 1 3 dataset if you forgot the baseline correction Notice the large artefact at zero frequency due to the DC offset 4 22 W J A m a i Processing the FID o GHz Figure 4 29 FFT of the Section 4 2 dataset without baseline correction No left shift is required The 10 G offset causes the signal to appear at 10 x 2 8 MHz 28 MHz or 0 028 GHz in the display Notice the absence of the artefact due to quadra ture detection imbalances The phase cycling has suppressed the artefact Also notice the admixture of absorption and dispersion Phasing the Spectrum 4 3 4 Even though the Signal Phase was adjusted properly the off resonance FIDs produce spectra that are not properly phased Because of the deadtime we cannot acquire the FID data from the very beginning Collecting the data starting at the end of the deadtime is equivalent to a time shift We have already seen the effect of a time shift on the frequency domain spectrum in Equa tion 2 22 and Figure 2 23 A linear phase distortion is intro duced into the frequency spectrum as a consequence of the time shift Because we only have one EPR line we can still corre
176. llbar on its right hand side is used to viewed the other lines The size of the message display area can be changed by clicking and dragging the resizing button so that you can view multiple lines To close the PulseSPEL Programming Panel double click the close button in the upper left hand corner of the window E 580 User s Manual D 29 PulseSpel Programming Panel Buttons Document Display Area Resizing Buttons Message Display Area Figure D 9 The PulseSPEL Programming Panel D 30 shg PulseSpel Programming Panel File New Program Load Program D 4 1 This drop down menu contains commands associated with file handling tasks such as saving and loading programs and variable definitions File New Program Load Program Save Prayram as New Variable Definitions Load Variable Definitions Save Variable Definitions Save Variable Definitions As PulseSPEL Path Figure D 10 The File menu Clears the presently loaded PulseSPEL program Loads a new PulseSPEL program A dialog box appears allow ing you to select a program file One means of selecting a pro gram is to navigate to the desired path in the Group box and double click the program filename in the Contents of this Group box Another method is to type the path and program filename into the Path and File boxes and then click Load Pulse program files have the three letter
177. lseSPEL program Click the Validate button The pulse program is not only compiled but also each step is checked to verify that it is within the limits of the spectrometer capabilities If successful the statement Second pass ended appears in the message window Close the PulseSPEL window Double click the close button pO Acquisition Trigger T 2 fe Figure 6 30 Variable definitions for the modified 2Dstd exp 5 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 6 26 Set the variables to the values indicated in Table 6 5 6 32 i Three Pulse ESEEM Variable Value d1 96 ns d2 400 ns dO Determined in Step 14 of Section 6 2 1 d30 16 ns d31 4 ns pO 16 ns h 10 Table 6 5 Variable values for the stimulated echo decay experiment Press the Run button The spectrometer will acquire the stimulated echo decay This acquisition will take a while because it is a two dimensional experiment Save the spectrum Phase the data The real data should be a slowly decay ing exponential and the imaginary data should be flat If you followed the directions in Section 5 2 correctly phasing should not be necessary If there is an appreciable amount of signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat E 580 User s Manual 6 33 Three
178. ly active column This command sets up multiple pulses First highlight an entry in the column containing the desired pulse length Select Repeat Group and a dialog box appears The Number of Periods is the number of copies of that column to be made including the orig inal column The Period Separation is the time spacing between the newly created pulses If you require pulses that are not equally spaced Period Separation Inc allows you to sequentially increase the time between pulses by that value agParfilf Number of Periods 2 t kb a Beal a p Help Period Separation ns 0 Period Separation Inc ns 0 OK Cancel Figure C 6 The Repeat Group dialog box The Patterns Panel Number of Points C 2 2 You may find that sometimes the acquisition software displays the following warning Attention Q ERROR user in e680 Experiment ftEpr StartPisPrg Pattem RAM size exceeded x ox wer Figure C 7 Warning of too many pulses or too many points The cause of this warning is too many pulses and points Your experiment must conform to the following condition 4 x Number of Pulses 2 x Number of Points lt 128 000 The Number of Pulses is simply the total number of pulses that you have programmed The Number of Points is the number of points in the spectrum for a 1D spectrum or the number of points in one slice of a 2D spectrum
179. microphonics from a sample that moves The sample tube rests on the hole of the sam ple support See Figure A 21 Figure A 21 How the sample support stabilizes the sample To install the sample support screw the support gently into hole in the bottom of module See Figure A 22 Don t force the screw Figure A 22 Inserting the sample support A 24 Microwave Data Microwave Data A 6 Table A 3 shows the microwave characteristics of all the X band resonator modules The two Qs listed per resonator are for matched and over coupled resonators C is the B microwave magnetic field conversion factor per Watt of microwave power Resonator Module v ompty Loaded Q Cc GIW GHz ER 4118 X MD5 9 7 4000 4 2 150 1 0 ER 4118 X MS5 9 7 500 2 0 150 1 2 ER 4118 X MS3 9 7 500 4 0 150 2 4 EN 4118 X MD4 9 7 500 1 8 Pulsed ENDOR 150 1 0 Table A 3 Frequency Q and conversion factors for the X band resonator modules E 580 User s Manual A 25 Notes A 26 sD BROKER EPL Integration B Integration of the area under an echo for field swept spectra is a very convenient means to acquire EPR spectra It relies on the fact that integration suppresses high frequency oscillations from off resonance effects This suppression results in improved reso lution compared to only detecting the echo height The E 580 spectrometer performs the integration by digitizing the echo and numerically integrating
180. mount of signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat W J A m a 5 34 i Two Pulse ESEEM Two Pulse ESEEM 5 6 The two pulse ESEEM experiment is an echo decay measure ment with modulation of the echo intensity by the nuclei l Follow the instructions of Section 5 5 1 We are using that experiment as the setup experiment for the present experiment Remember to record the time at which the top of the echo occurs Repeat steps Steps 9 and 10 of Section 5 5 1 Set d1 to 96 ns instead of 400 ns Verify that the echo is not clipped If it is clipped reduce the VAMP gain until the echo is no longer clipped Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file echodecay2phi exp and click the Load button agPgload Group Contents of this Group 2Dstd_set 2p_eseem 4pulse_eseem Apulse_eseem2d echo2phi echo_fs echo_ir fideycle fidcycle_bestep 7 PulseSPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File echodecay2phi exp show Filenames 4 Cancel Help Load Button Figure 5 38 Selecting the PulseSPEL program E 580 User s Manual 5 35 Two Pulse ESEEM
181. mple The sample tube particularly if it is filled with a frozen aqueous solution may burst when it warms up Insert an empty sample rod and tighten the collet nut A 16 W J A m a i Variable Temperature Operation Gas Flow for Room Temperature Operation A 3 3 A Signal channel cali bration may easily supply sufficient modulation ampli tude to cause heat ing problems If you use the resonator in CW mode i e using field modula tion in a cryostat at room temperature you may need to supply some gas flow Modulation amplitudes greater than five Gauss heat the resonator and the cryostat prevents the resonator from dissipating the heat In order to remove the heat and prevent damage to the resonator dry nitrogen must be blown through the cryostat This is easy to accomplish with the ER 4118CV cry ostat by supplying the gas to the glass transfer line If you are using an ER 4118CF cryostat you must use a dummy transfer line to ensure proper gas flow Simply pushing the gas into the cryostat side arm will not cool the resonator E 580 User s Manual A 17 Changing Resonator Modules Changing Resonator Modules A 4 One of the attractive features of the FlexLine series is the ability to change the resonator module Only one probehead support is required for many different resonator modules This section guides you through changing the resonator module Removing a Resonator Modu
182. mplitude Adjustment 15 Adjust Channel 1 Offset until the smallest ampli tude pulse has its top at the upper edge of the SpecJet display In this case the X pulse is weakest but it can easily be any of the other pulses as well 6 000 4000 2 000 2 000 4000 ae ee Peal i e 0 500 1 000 1 500 2 000 0 Timej ns J Figure F 5 Setting the offset for easy amplitude compari sons Phase amp Amplitude Adjustment 16 Adjust the LVL knobs until all the amplitudes are identical Figure F 6 Equalizing the pulse amplitudes E 580 User s Manual F 7 Phase amp Amplitude Adjustment Adjust the phase of the X pulse until it is maxi mum and negative 2 000 T T j T T T T T j 1 500 2 000 Time ns 0 500 1 000 Figure F 7 Adjusting the phases 18 19 Adjust the phase of the Y and Y pulse so that they are nulled Verify the Y and Y pulses are z out of phase Turn the TM knob slightly to see if one signal goes up and the other goes down If not null the signals again with the TM phase knob and adjust the Y phase knob until the next null is obtained Repeat until successful Phase amp Amplitude Adjustment 20 Adjust the TM phase to individually maximize each of the pulses Verify that all of the pulses have equal amplitude when the TM phase maximizes the pulse Adjust the level knobs until all the pulses are equal in amplitude
183. n in Fourier trans form spectroscopy We start offin Figure 2 23 with a purely real signal remember that a symmetric signal has a purely real Fou rier transform and after the time delay we obtain an oscillating mixture of real and imaginary components Because of the recip rocal nature of Fourier transform pairs similar behavior in the time domain signal is observed when the frequency is shifted in the frequency domain signal F Re Im Lb A 1 1 EELEE pre Figure 2 23 The time shift properties of the Fourier trans form E 580 User s Manual 2 27 Pulse EPR Theory The Convolution Theorem The convolution integral appears frequently in a number of sci entific disciplines The convolution of two functions is defined as 00 f t g t f t g t t dt 2 24 00 It can also be shown that f t g t g t f t It is difficult to envision exactly what the convolution is doing but it can be interpreted loosely as a running average of the two functions In the limit of a Dirac delta function i e a spike the convolution can be graphically represented as in Figure 2 24 We are placing a copy of our function at each of the spikes fh A AA Figure 2 24 The convolution of two functions The convolution theorem states that the Fourier transform of the convolution of two functions is equal to the product of the Fou rier transforms of the individual functions We no
184. n than the lower step Step 138 00000 N Average 137 6 Step 137 000 0 Figure 2 61 Improvement in amplitude resolution with sig nal averaging ten times As we average more we obtain better amplitude resolution Amplitude Resolution Bits L fi J 1 12 4 8 16 32 Number of Accumulations Figure 2 62 Dependence of amplitude resolution on the number of averages 2 60 Pulse EPR Practice Resonators 2 2 4 Resonators are perhaps the most critical element of a pulse EPR spectrometer They convert the microwave power into B and also convert the transverse magnetization into a FID or echo In CW EPR we typically use high Q cavities because they are effi cient at converting spin magnetization into a detectable signal This is not an option for pulse EPR because high Qs contribute to long deadtimes The Q is the ratio of the energy stored and the power dissipated in the resonator We need to dissipate the high power microwave pulses very quickly the so called ring down time so that it does not interfere with the detection of the very weak FID and echo signals Another requirement of the resona tor is bandwidth so that we do not distort broad EPR signals We therefore have two very good reasons to keep the Q as low as possible We still need to convert the microwave power into B and the transverse magnetization into signals efficiently The efficiency is proportional to VQ We cannot
185. n the pulse program See below There are 32 RF variables DFO DF31 that store frequency values to be used in pulse ENDOR experiments In addition there are two variables RF1 and RF2 that determine the fre quency of the first and second channels of the ENDOR unit respectively The default units are kHz but you can also specify values in MHz Note that you must have the optional pulse ENDOR accessory in order to actually use these variables The Structure of PulseSPEL Programs D 1 2 Definitions Section Pulse programs are stored on the hard disk in files with the three letter exp extension The programs are subdivided into three distinct sections the definition lists and experiment section Each program must begin with a definition section in which the dimension of the dataset is declared by the dim statement The numbers in square brackets after dim are the dimensions of the x and y axes Here is a definition section for a one dimensional dataset with 512 points begin defs dim 512 1 end defs C gt BROKER LS The PulseSPEL Programming Language Lists Section The start of the definition section is indicated by begin defs and the end by end defs The definition section must be followed by a lists section This contains information regarding the phase cycling of the micro wave pulses and the detection The start of the lists section is indicated by begin lists and the end by end lists There are 16 ph
186. nce Arm On button so that it is green active 17 Maximize the bias Adjust the bias slider until it is completely on the right hand side See Figure 3 5 18 Set the CW attenuator to 60 dB See Figure 3 5 19 Set the HPP attenuator to 60 dB Make sure that the HPP attenuator on the pulse bridge controller is set to 60 dB See Figure 3 10 HPP Attenuator BRGORER PULSE BRIDGK ONTROLLER o o o Co cw LPP bow WAKEUP 5V 15V one fo fe e 6 ie 6l 10l 0 IND ALT DIG o o o READY 5V 15V 20V Figure 3 10 Buttons on the pulse bridge controller The but tons that should be on activated for pulse oper ation are highlighted E 580 User s Manual 3 7 Tuning Up 20 Press the CW button The LED will go out 21 Press the QUAD button The LED will light when it is activated This switches the detection from the CW detec tor to the quadrature detector 22 Press the HPP button The LED will light when it is It is extremely important to press activated This switches the excitation from CW to pulse the QUAD button mode first before the HPP button is pressed 23 Press the AMP button The LED will light when it is Performing these activated This turns on the preamplifier two operations in reverse order may lead to damage to the CW detector Saf
187. ng areas are properly ven tilated They should be equipped with powerful blowers and fume heads Store chemicals safely Avoid integrating containers of chem icals that may result in dangerous combinations Practice good housekeeping in work and storage areas Clean up spills and refuse promptly Do not leave volatile combus tible or acidic liquids exposed on counters benches or other work areas Make certain all chemical containers are properly labeled and classified and that especially hazardous materials are appro priately designated with clearly understood decals or warn ings Never taste or inhale unmarked chemicals E 580 User s Manual Microwave Safety e All laboratories should be equipped with fire doors fire extinguishers fire smothering materials and sprinkler sys tems or showers as well as a detailed fire safety plan Microwave Safety 0 3 As long as the microwaves are contained in metal structures microwaves can be very safe Here are some precautions which if followed will eliminate the possibility of injury due to the microwaves e Do not have an open waveguide or detached semi rigid cable when the microwave power is on e Switch the bridge to standby when you remove or change EPR cavities e Never look down an open waveguide or detached semi rigid cable when there is microwave power The eyes are very sus ceptible to damage from microwaves vi C gt BROKER COO Table of
188. nguage for performing pulsed EPR experiments The pulse tables are convenient for setting up many easy experi ments but they also restrict your choice of experiments Puls eSPEL enhances the capabilities of the E 580 spectrometer by offering the following expanded capabilities e User defined phase cycling e Two dimensional time domain experiments such as HYSCORE and EXSY e Field steps to eliminate baseline effects e Standardization and simplification of data acquisition meth ods You can create your own customized pulse programs within PulseSPEL In addition PulseSPEL comes with several standard libraries of pulse programs They can be found in the xepr Files PulseSPEL sharedPulseSPEL directory There are sev eral subdirectories for the old style PulseSPEL programs and one for the new style programs PulseSPEL2000 The indi vidual directories are classified by the number of MPFUs Microwave Pulse Forming Unit For example SPEL1 is for spectrometers with one MPFU SPEL2 for those with two MPFUs etc There is also a directory PESPEL for pulsed ENDOR experiments E 580 User s Manual The PulseSPEL Programming Language The PulseSPEL Programming Language D 1 Variable definitions and pulse programs are kept separate in PulseSPEL In this way the pulse program needs to be compiled only once If delays or pulse lengths need to be changed only the variable values need to be changed Variable Definitions D 1 1
189. ns Tau 442 69201 3 Transformations fit Tau yes no noe ves na M O Eeee Structure gt Polynomial Exponential Decay XSophe Splines ae leae 4 Command Automatic _ Exponentials Po 5 adel Saturation Curve Fit Cose Setup Help Spectral Titration Exponential Decay SS Biexnonential Decav Figure 5 42 Fitting an exponential to the echo decay 12 Move the Result dataset to the Secondary dataset 13 14 Subtract the Primary and Secondary datasets Move the Result dataset to the Primary dataset lj Mil I alt hl T o T T T T T 500 1000 1500 2000 2500 3000 3500 4000 Figure 5 43 ESEEM oscillations observed after the echo decay is subtracted E 580 User s Manual 5 39 Two Pulse ESEEM 15 Click the Window Function task button The Win dow Function task bar then appears TASKS WINDOW FUNCTIONS Baseline Correction Window Start Peak Picking Function HEA Integration Button FFT Real gt Fitting EEPE Filtering TE Hamming xSophe ae Function Gellss Button Save Status Te mE C FT FFT Real lt ji one mm Figure 5 44 The Window Function task bar 16 Click the Hamming button in the Window Func tion task bar The Hamming window dialog box appears prWinHamming Slice current vall x Max 4088 Paa xo fo Ap
190. ns Monitoring Een 10 000 5 000 10 000 l r 0 500 1 000 1 500 2 000 Time fns Figure 4 3 A properly phased FID of a single EPR line 7 Optimize the microwave power Adjust the HPP attenuator to maximize the FID 8 Change from Run from Tables to Start Transient mode Click the Start Transient button in the Acquisi tion panel See Figure 4 4 i Acquiring a FID with the Pulse Tables Start Transient is a misnomer You must have the pulse pro grammer already running to acquire the FID If the FID is not acquired click the Start button next to the pulse tables in the Patterns panel FTEPR Parameters Patterns Field Acquisition l Options ABSCISSA QUANTITIES AND SIZES X Axis Size 1024 a X Axis Quantity Time y Y Axis Quantity Magnetic Field y Y Axis Size 1 ACQUISITION MODE v Run from Tables 4 Quadrature Detection w Run from PulseSPEL m Read Transient Start Transient PulseSPEL AR ISITION age Start Transient Exper Button Mh Jase PulseSPEL Variable Phase Program Normal y Close PulsesPEL Help Figure 4 4 Switching to Start Transient mode 9 Press the Run button The spectrometer then acquires the FID and it appears in the viewport gt ofj mieg Run Button Figure 4 5 The Run button 10 Save the sp
191. ns inter act with each other resulting in mutual and random spin flip flops Molecular motion can also contribute to this relax ation These random fluctuations contribute to a faster fanning out of the magnetization This broadening mechanism results in lorentzian lineshapes which we shall discuss in the next section The decay of the transverse magnetization FID from this mechanism is in general exponential M t e 2 13 where T gt is often called the spin spin relaxation time A Few Fourier Facts 2 1 3 So far all our discussions have been very geometric It was men tioned that the information about the frequency spectrum was somehow encoded in the transverse magnetization in the rotating frame One means of reconstructing the frequency spectrum is to study the time behavior of the transverse magnetization See Figure 2 19 The component of the transverse magnetization along the y axis will vary as M t M cosAat 2 14 where Aq is the frequency offset wg and t is the time after the microwave pulse The component along x will vary as M t M sinAot 2 15 E 580 User s Manual 2 21 Pulse EPR Theory Cos Aot Sin Aot Figure 2 19 Time behavior of the transverse magnetization A common mathematical convenience is to treat these two com ponents as the real and imaginary components of a complex quantity ae 2 16 M t M where e cosp i sind 2 17 and i wl
192. nsider a large number of electron spins in a magnetic field B aligned along the z axis See Figure 2 2 The elec tron spins are characterized by two quantum mechanical states one with its magnetic moment parallel to B and one antiparal lel The parallel state has lower energy and at thermal equilib rium there is a surplus of electron spins in the parallel state according to the Boltzmann distribution Therefore there should be a net magnetization parallel to the z axis The magnetization is the vector sum of all the magnetic moments in the sample The electron spins are still precessing about the z axis however their orientations are random in the x y plane as there is no rea son to prefer one direction over another For a very large number of electron spins the various transverse i e in the x y plane components of the magnetic moments cancel each other out The result is a stationary magnetization Mo aligned along Bo Figure 2 2 The Larmor precession and the resultant station ary magnetization E 580 User s Manual 2 5 Pulse EPR Theory Magnetization in the Rotating Frame EPR experiments are usually performed with a resonator using linearly polarized microwaves The microwave resonator is designed to produce a microwave magnetic field By perpendic ular to the applied magnetic field Bg In most cases B lt lt Bol Linearly polarized microwaves can be thought of as a magnetic field oscil
193. ntered into the pulse Q tables and the HPP attenuator should be about 5 6 dB The No of Averages in the SpecJet panel should be set to 100 No of Points set to 512 and Timebase ns set to To calculate the 4 ns and Repetitive Mode selected fiel Pa e 2 Set the magnetic field We set the field purposefully wave frequency in off resonance in Section 3 3 to test for ringdown Set the GHz by 2 8 to obtain center field to approximately 3440 G or to the value cal the field in culated with the formula in the hint with a sweep width Kilogauss Multiply of 100 G You will probably see a FID See Figure 4 1 by 1 000 for the value in Gauss lh 5 000 5 000 aie ttn l Mi 5 000 en nen 5 000 4 M Wy i 0 500 1000 1500 Bisa a 0 500 1000 1500 Turena Figure 4 1 A clipped FID and one with a properly adjusted VAMP gain g pp i Acquiring a FID with the Pulse Tables The slower the oscil lations become the closer you are to being on resonance See Equation 2 23 and Figure 2 31 A You will need to adjust the sample length slightly longer than in Figure A 8 so that you can move the sample sufficiently downwards Set the VAMP gain Adjust the gain so that the ampli fier or digitizer is not clipped See Figure 4 1 Adjust the field until you get a single exponen tial We see the oscillations in the FID because we are not on resonance Once we are on resonance with the single EPR lin
194. o 16 ns Y pulses 400 ns apart First delete the X pulses from the pulses tables Start the experiment again The SpecJet display may look similar to the following figure If everything is perfect all of the echo should be in the imaginary channel and should be positive going There should be no signal in the real chan nel If not adjust the Y phase knob until the echo is pos itive going in the imaginary channel and the real channel has no echo signal 10 000 5 000 gt 10 000 2 000 ae aa ae le i ee ee ee 0 500 1 000 1500 0 Time ns Figure F 10 An echo from two Y pulses properly phased and on resonance Phase amp Amplitude Adjustment 3 Repeat Step 2 with two X pulses Adjust the X phase knob until the echo is negative going in the real channel and there is no echo in the imaginary channel 4 Repeat Step 2 with two Y pulses Adjust the Y phase knob until the echo is negative going in the imagi nary channel and there is no echo in the real channel 5 Record the level and phase knob settings of each channel E 580 User s Manual F 13 Notes F 14 Index Symbols 2 C 18 2 C 18 A abscissa quantities and sizes C 10 to C 11 x axis quantity C 10 size C 11 y axis quantity C 10 size C 11 acquisition modes C 11 quadrature detection C 11 read transient C 11 run from PulseSPEL C 11 run from tables C 11 start transient C 11 trigger C 14
195. o change a variable value type variable name lt Space gt followed by the desired value into the Puls D 26 sD BROKER CoO Setting up a PulseSPEL Experiment eSPEL Variable box and then press the Enter key If you wish to verify that the variable value has indeed changed type in the variable name and press the Enter key to view the new value Magnetic Field yl PulseSPEL Variable Box Figure D 7 Editing PulseSPEL variables E 580 User s Manual D 27 Setting up a PulseSPEL Experiment 9 Press the Run button The spectrometer then runs the pulse program Run Button Figure D 8 The Run button D 28 i PulseSpel Programming Panel PulseSpel Programming Panel D 4 To open the PulseSPEL Programming Panel click the Puls eSPEL button in the Patterns panel of the FT EPR Parame ters window The PulseSPEL Programming Panel functions much like any standard text editor allowing you to select text with the cursor as well as cut and paste The important components of the panel are labeled in Figure D 9 The document display area contains the material to be edited or compiled The area can either contain the PulseSPEL variable definitions or the PulseSPEL program The Show Program or Show Var Def buttons determine which is displayed The message display area shows messages from the compiler such as error messages By default only one line at a time is dis played and the scro
196. on delay ax increment acquisit acq sgl next i dx dx d30 next x end exp ion delay Figure 6 23 Modified PulseSPEL programs for a stimulated echo setup experiment Added and modified sections are highlighted E 580 User s Manual 6 25 Three Pulse ESEEM Button Validate Button Close Validate the edited PulseSPEL program Click the Validate button The pulse program is not only compiled but also each step is checked to verify that it is within the limits of the spectrometer capabilities If successful the statement Second pass ended appears in the message window u fin ig JAAR g g E 5 AH AH f z E E E o itt g Compile Validate 101 a Help On Selection PulseSPEL Programming Panel 2Dstd_set exp dir lusripeopleirtwieprFilesiPuiseSPEL sharedPuls File Edit Search Compile Properties Options stimulated echo experiment ay program to evaluate timing and phases begin defs dim s 512 1 dimension of data array sx sy end defs begin lists phil x x x x phase program for 1st pulse ph2 x x x x phase program for 2nd pulse asgl a a a a sign program for RE part bsg1 b b b b sign program for IM part end lists begin exp SPT QUAD single point detection sweep x 1 to sx shot i 1 to h po ph1 1st pulse and phase progr dl constant pulse separation po ph2
197. orrespond to the dataset definition for the experiment definition exp D 16 sD BROKER oD The PulseSPEL Programming Language An Example Here is a standard PulseSPEL 2PESEEM EXP program that you can find in the sharedPulseSPEL Stan dard PulseSPEL2000 SPEL2 directory t n T i 2 Pulse EM Programs PA r F begin defs dim s 512 dimension of data array sx sy for set up diml s 1024 dimension of data array sx sy for fieldsweep dim2 s 512 dimension of data array sx sy for ESEEM dim3 s 256 128 dimension of data array sx sy for ESEEM vs field end defs r F begin lists none phi x ph2 x asgl a bsgl b end lists begin lists1 2 step phl x x ph2 x x asgl a a psal b b end listsl begin lists2 16 step phl x x y y x x y y ph2 x x y y x x y y PY y X AEX SY ty EX SK asgl ta a b b ta a b p a ta b b a a b b bsgl b b a a b b a ta b b a a b tb ta a end lists2 E 580 User s Manual D 17 The PulseSPEL Programming Language r r Standing begin exp 2P ESE shot i 1 to h d9 pO phi d1 p1 ph2 d1 do dig sgl next i end exp 2 Puls Echo for 2 Pulse Set Up Setup TRANS QUAD begin expl 2P ESE Field Sw Pp G Field Sweep for k l to n Ne Ne Ne Ne Ne Ne N
198. ort mairena a Se ee eee La GEER ZaEWR aEnnT ee 3390 M0 W0 MWA MW 340 350 M WWO XO Field G Figure 5 21 The field swept echo detected EPR spectrum of coal Save the spectrum Phase the data The real data should be an EPR absorp tion spectrum See Figure 5 21 and the imaginary data should be flat If you followed the directions in Section 5 2 correctly phasing should not be necessary If there is an appreciable amount of signal present in the imaginary data follow the directions in Section 4 3 4 and phase the spectrum until the imaginary trace is flat 5 20 W J A m a i T2 Measurements T Measurements 5 4 In this experiment we shall measure the Ty of the coal sample from its echo decay We shall monitor the echo height as we increase the time between the two microwave pulses in 8 ns steps The SpecJet digitizes the signal in single point mode Acquisition Trigger J 2n i l 3 l l Figure 5 22 The echo decay experiment l Follow the instructions of Section 5 2 There is one exception set the position of the second x pulse to 96 ns Determine the time at which the top of the echo occurs Use the cursor readout on the acquired echo to measure the time Record this value EM I v a0 Secnaarys Sas sirj H 2000 Intensity LT Ins Figure 5 23 Determining the time of the top of the echo with the cursor rea
199. ounter clockwise fashion Conversely if Aw lt 0 the magnetization is lagging and will rotate in a clockwise fashion Zz z M y y Z On resonance Off resonance Figure 2 10 The magnetization in the rotating frame exactly on resonance and Aw off resonance E 580 User s Manual 2 11 Pulse EPR Theory Quadrature detec tion to be discussed in the Detection sec tion on page page 2 44 is a means for measur ing both transverse magnetization com ponents in the rotat ing frame This gives us the required amplitude and phase information to trans form the signals into a frequency repre sentation This frequency behavior gives us a clue as to how the EPR spec trum is encoded in the FID The individual frequency compo nents of the EPR spectrum will appear as magnetization components rotating in the x y plane at the corresponding fre quency Aw If we could measure the transverse magnetization in the rotating frame we could extract all the frequency compo nents and hence reconstruct the EPR spectrum A second consequence of not being exactly on resonance is that the microwave magnetic field B actually tips the magnetization into the x y plane differently because By does not disappear when we are not on resonance We determined that Bg disap pears in the rotating frame when we were on resonance because our magnetization is no longer precessing When we are off res onance the magnetiz
200. p define trigger increment end of sweep loop output of scans done EM vs BO INTG QUAD field sweep on y axis E 580 User s Manual D 19 The PulseSPEL Programming Language for k l to n totscans n sweep x 1 to sx shot i l to h d9 po phl d1 dx pl ph2 dl do dx acq sg1 next i dx dx d30 next x dx 0 scansdone k next k next y end exp3 averaging loop for time scan output of total number of scans DAF lst pulse and tau tau increment sweep loop for time scan accumulation loop phase program phase program onstant acquisition delay ncrement trigger position Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne Ne 2nd pulse and tau c i acquisition end of accumulation loop define trigger increment end of sweep loop output of scans done The first dim statement corresponds to the dataset for the first exp statement the second dim1 statement corresponds to the dataset for the exp1 statement and so on The def statement is followed by the individual lists section Each is given a name Finally come the individual exp sections each of which is given a name Note that the first dim lists and exp statement all must not have a number suffix In the next section we shall see ho phase cycles and experiments when acquisition w to choose the different we perform a PulseSPEL D 20 The PulseSPEL Acquisition Panel The PulseSPE
201. pa Figure 5 32 Validating the PulseSPEL program 8 Close the PulseSPEL window Double click the close button E 580 User s Manual 5 29 Field Sweeps with PulseSPEL Acquisition pO p1 k Trigger NIA Ser d1 d1 dO dx Figure 5 33 Definition of the variables for echo2phi exp 9 Set some PulseSPEL variable values Edit and ver ify the values of the variables in the PulseSPEL variable box See Figure 5 34 Set the variables to the values indicated in Table 5 1 Variable Value d1 400 ns do 0 ns d30 4ns pO 16 ns p1 32 ns h 10 n 1 Table 5 1 Variable values for the setup experiment W J A m a 5 30 Field Sweeps with PulseSPEL FT EPR Parameters Pattems Field RF Acquisition l Scan l Options l ABSCISSA QUANTITIES AND SIZES X Axis Quantity me x X Axis Size 512 Y Axis Quantity Magnetic rea Y Axis Size 1 ACQUISITION MODE Sa ea ees QuatatireDetecton FT PulseSPEL wv Read Transient Variable wv Start Transient Box PulseSPEL ACQUISITION PulseSPEL Program SPEL2 fidcycle_bestep exp PulseSPEL Variable d0 40 ns Experiment EXP y Phase Cycling LISTS y Phase Program Normal y PulseSPEL Help Figure 5 34 Editing PulseSPEL variables 10 11 12 Press the Run button The spectrometer then acquires the echo and it appears
202. part requires looking at the echo from the coal sample It is strongly advised to only perform these adjustment after the spectrometer has warmed up for several hours Setup F 1 In order to perform this adjustment we will need to rearrange two cables and set some knobs on the pulse bridge controller l Locate the RG 58 cable labeled TM It should be connected to a BNC connector labeled TM on the back of the bridge Locate the RG 58 cable labeled DS1 It should be connected to the left channel of the SpecJet Disconnect DS1 from the female female BNC barrel connector Connect TM to the female female BNC barrel connector E 580 User s Manual Phase amp Amplitude Adjustment 5 Set all the LVL level knobs to 10 0 on the pulse bridge controller o o o ojo sod ogee PULSE BRIDGE CONTROLLER STAB o o b Monitor 1 ecw d SE Ex CO RA TRANS LEV MONITOI P MONITOR 2 Ro F J Se A REF BIAS SEB GER GES EE 0 ER Er NA O O Oo Se NES REF BAL x STAB FREQ VIDEO AMPLIFIER GAIN d8 BANDWIDTH MHz poooD D000 Oa LVL ATTENUATION dB Figure 6 1 Coarse Adjustment Important knobs on the pulse bridge controller 6 1 Ww O eS ON e Set all the phase
203. pecJet amplitude video amp resolution used gain 3 bit 8 steps 12 dB 4 bit 16 steps eee 18 dB 5 bit 32 steps 24 dB 6 bit 64 steps 30 dB 7 bit 128 steps 36 dB 8 bit gt H 256 steps SpecJet full scale 0 5 V Figure 2 59 The effect of video amplifier gain on the digi tized signal 2 58 Pulse EPR Practice Signal Averaging A commonly used technique to increase the signal to noise ratio of a signal is to repeat the experiment and average the results of the repeated experiments The signal will grow linearly whereas the noise will grow with the square root of the number of aver ages Over all the sensitivity increases with the square root of the number of averages 3 SON 1 eventing I eter 4 2 E 8 Meo Figure 2 60 Signal to noise improvement as a function of the number of averages Signal averaging not only increases the signal to noise ratio but its also increases the effective dynamic range If we need to resolve two signals that have almost the same voltage the noise actually helps when we signal average The noise randomly per turbs the signal up and down so as we average the signals we fill the space between the 256 equally spaced steps described in E 580 User s Manual 2 59 Pulse EPR Practice the previous section If the signal is closer to one step than the other statistically the upper step will be measured more ofte
204. periments After clicking Cal culate the required pulse timings are calculated by the software If you need to edit the entries click Restore In this mode you cannot start a pulse sequence until you have clicked Calculate This ensures that the pulse sequence for the hardware is correct and safe The third mode Setup is only used for initial calibration pur poses during installation of the spectrometer For the sake of safety it should only be used by trained Bruker personnel sD BROKER EPL The Options Panel Figure C 13 Manual mode of the pulse tables All Visible If All Visible is active green all the channels in the pulse con figuration tables See Appendix E will be accessible through the channel selector E 580 User s Manual C 17 The SpecJet Display The SpecJet Display SpecJet Display 0 5 000 10 000 15 000 0 Time ns AVERAGING TIME BASE No of Averages 100 Time Base ns 4 0 Averages Done fo No of Points 4096 I Stop Close Settings Ea Figure C 14 The SpecJet Display 2 Reduces the SpecJet Display by a factor of two 2 Magnifies the SpecJet Display by a factor of two C 7 W J A m a The SpecJet Display FS Run Stop Close Settings Averaging No of Averages Averages Done Time Base Time Base No of Points Sets the SpecJet Display to full sca
205. ply n Close Button EA E0 cos PI x y where Button a Xx X lt x0 gt XW lt xMax gt lt x0 gt Apply Close Help Figure 5 45 The Hamming window dialog box 5 40 i Two Pulse ESEEM 17 Click the Apply button followed by the Close but ton The default values work well for this example Hefei Fs window Function 600 400 nA 200 P et o hirinn nasarar 200 400 sR Ro 500 1000 1500 2000 2500 3000 3500 4000 ei Le IT i Figure 5 46 The Hamming function with a windowed echo decay 18 Transfer the Result dataset to the Primary dataset After you click Close a dialog box appears asking if you want to Move result to input Click Yes Please decide Move result to input Figure 5 47 Transferring the Result dataset to the Primary dataset E 580 User s Manual 5 41 Two Pulse ESEEM 19 Select the FFT command Click its button in the Transformations submenu of the Processing menu Diff amp Integ F Filtering 2 Algebra Peak Analysis Complex Window Functions FFT Command Transformations F fnaganj _ Zero Filling nies prFFTic Fitting lt FFT PERAIRE Sreto gt FFT Rea ste 2D FFT tee f ProDeL Cross Term Averaging Automatic 7 Convolition ua iep undo Deeenvelition iy Symmetrization Invert Abscissa
206. ppears Baseline Correction Button TASKS jaseline Correction Peak Picking Integration Fitting Window Function Filtering XSophe Sea Polynomial Button BASELINE Polynomial Spline Retum Figure 7 15 Selecting polynomial baseline correction i The HYSCORE Experiment A y The exponential decay is so slow that a second order poly nomial approxi mates the echo decay fairly well 13 Fit a second order polynomial to the baseline Click the 2nd Order button in the task bar A fitted func tion appears Define Region Button Return Button BASELINE POLY Start Define Region 2nd Order C Baton me aha Ch COENE eee Ses Gabe aan et ee Subtract Line Subtract Line Button Figure 7 16 The polynomial baseline fitting task bar Click the Slices All button This ensures that the base line subtraction is performed on each of the slices of our two dimensional dataset If you do not perform this step you will receive an unpleasant surprise Your 2D dataset is converted into a 1D dataset 14 prFitSquare Slice v current gt all Ft Function y ax 2 bx c Figure 7 17 The 2nd Order dialog box E 580 User s Manual 7 15 The HYSCORE Experiment 15 Subtract the baseline Click the Subtract Line button in the task
207. r You may choose to redo the last undo operation or redo all the undo operations since you loaded the particular variable defini tions or PulseSPEL program file Edit Undo Redo pezecon cut Copy Paste Select Line at Number What Line Number Show Caret All Undos Figure D 18 The Redo submenu Cuts the selected text in a buffer for pasting Copies the selected text in a buffer for pasting Pastes the text in the buffer into the present PulseSPEL program or variable definitions When clicked a dialog box appears requesting a line number The default value is the current line number where the cursor is Enter a line number and click select The cursor will be moved to the selected line agPgSelectline Line number 1 L Figure D 19 The Select Line at Number dialog box Displays at the bottom of the window the line number where the cursor is presently located E 580 User s Manual D 37 PulseSpel Programming Panel Show Caret Not implemented Search D 4 3 This drop down menu contains commands associated with searching and replacing text Search String Search Selection Forward Search Selection Backward Replace String Figure D 20 The Search drop down menu Search String Searches the present program or variable definitions for a string Type the string to be searched for in the Search String box The search direction can be con
208. r d1 value for field sweeps If you are working with samples having very long T s very common at low temperatures you may have to increase the SRT Shot Repetition Time in order to see a signal See Equation 2 12 5 46 i Three Pulse Experiments 6 This chapter describes two types of three pulse experiments The first is an echo detected inversion recovery experiment The sec ond is a stimulated or three pulse echo experiment We shall use the Bruker supplied coal sample for both experiments As we discussed on page 2 38 three microwave pulses lead to five ech oes In order to eliminate the unwanted echoes we shall use the phase cycling capabilities that PulseSPEL offers us The inversion recovery experiment is similar to the inversion recovery experiment described in the previous chapter except we are using a two pulse echo to detect the recovering magnetiz taion Because the T of the coal sample is very long we need to take some special precautions regarding our PulseSPEL variable values We shall intentionally make a few mistakes to view the error messages and learn to correct the problems We shall also learn how to edit PulseSPEL programs to customize the standard experiments so that they meet our specific needs The stimulated echo experiment will be our first two dimen sional pulse experiment We shall acquire and process three pulse ESEEM data in which the second dimension is our tau value
209. r the TWT 3 Set the VAMP Video Amplifier bandwidth to 200 MHZ Press the right hand VAMP bandwidth button repeatedly until the LEDs under the 200 MHz label are lit See Figure 3 3 Set the VAMP gain to 60 dB If you have just turned the console on you will first have to press both VAMP gain buttons simultaneously until the two left most LEDs in the display are lit See Figure 3 3 This may require a few attempts Then press the right hand VAMP gain but ton repeatedly until the LEDs under the 60 dB label are lit W J A m a Tuning Up 5 Activate the CW and STAB buttons A lit LED indi cates that the button is activated Press the buttons until the indicator LEDs are lit CW Button VAMP VAMP Gain Bandwidth G ehGner PULSE BRIDGE CONTROLLER a _ o o fototo reek N oon Sete 2 2 2 o ibe AA ERR oe SEQ Ee E gt oa i ERR ER ER STAB Button Stabilizer Adjust ey Q MONITOR 2 REF BAL X ment Buttons Y w ats 5 GR N ASR EX ER ERR Vx Xo f AP e ie TER i 7T I P j H 8 i Oo Cw vd oo ee Figure 3 3 Important buttons on the pulse bridge controller Tuning Up 3 2 1 Click the tuning button The microwave tuning dialog box will appear See Figure 3 5 Create New Parameter
210. re carefully measured by the Bruker instal lation engineer upon the initial spectrome ter installation Changing these val ues can lead to unre liable operation or even worse damage to bridge compo nents This panel contains all the information for the automatic calcula tion of the delays and pulselengths to safely and correctly per form a pulse experiment The only value that you may have to adjust is the length of the Receiver Protection pulse also known as the defense pulse Never make the pulselength shorter than the installation value If you are performing experiments in which the resonator Q is higher than normal Q gt 100 the ring down of the cavity will persist longer Therefore the Receiver Protection pulse length must be increased in order to protect the preamp of the pulse bridge during the longer ring down time After increasing the Receiver Protection pulselength carefully perform the safety check See Section 3 3 If you see excessive ring down stop immediately and increase the HPP attenuation Increase the pulselength until you do not observe any ring down If any changes are made to the values in this panel you must click Apply before they take effect E 580 User s Manual Configuration and Timing Data Set Selection Data Set Load Save Delete TWT and RF TWT Minimum Gate Time TWT Maximum Gate Time TWT Recovery Time TWT Duty Cycle RF Duty Cycle E 2 1 The
211. riate maximum bandwidth listed in Table B 1 Maximum Time pase ne Bandwidth MHz 4 200 6 200 8 50 10 50 20 25 Table B 1 Timebases and their maximum bandwidths The top spectrum of Figure B 1 shows a correctly acquired spectrum with time base 4 ns bandwidth 200 MHz In the middle spectrum the 20 ns time base is too long Changing to a 25 MHz bandwidth results once more in a correct spectrum B 2 BROKER Timebase and Bandwidth 4 ns Timebase 200 MHz Bandwidth 60000 40000 200004 o4 20000 40000 4 60000 4 Intensity 0 80000 4 100000 120000 J 140000 J 160000 J 180000 T T T T 7 7 7 T T T T 3410 3415 3420 3425 3430 3435 3440 3445 3450 3455 3460 3465 3470 Field G 20 ns time base 200 MHz Bandwidth 60000 40000 J 200004 Artefact Artefact zl Inten 100000 120000 4 140000 4 160000 4 180000 J T T T T T T T T T 3410 3415 3420 3425 3430 3435 3440 3445 3450 3455 3460 3465 3470 Field G 20 ns Timebase 25 MHz Bandwidth 60000 5 400004 20000 4 20000 4 40000 4 60000 80000 4 Intensity J 100000 120000 140000 160000 180000 J T T T T T T T T T 3410 3415 3420 3425 3430 3435 3440 3445 3450 3455 3460 3465 3470 Field G Figure B 1 Effect of bandwidth and time base on field swept echo detected EPR spectra Note artefacts in middle spectrum E 580 U
212. rigger connection This button allows you to choose whether to trigger on the rising or falling edge of the External Trigger signal The amount of time the PatternJet will wait for an incoming External Trigger signal before stopping the acquisition and dis playing an error message The priorities of the external trigger repetition time and SRT Shot Repetition Time resolve themselves as follows The slower repetition time always has priority If you set the SRT to a value shorter than the repetition time of your external trigger the external trigger determines the repetition rate If your SRT is set longer than the repetition time of your external trigger the SRT determines the repetition rate E 580 User s Manual The Options Panel Pulse Patterns Pattern Control C 6 2 There are three options In general you will only use Auto mode In Auto mode you simply need to type in the entries into the pulse tables The software automatically calculates the pulse timings required to perform the experiment See Figure 2 51 In Manual mode the pulse timings are not automatically calcu lated Two more buttons Calculate and Restore appear in the panel Also The channel selector gains a number of other chan nels not present in Auto mode such as the TWT gate and the defense pulse This allows you to view all the actual delays and pulselengths used to control the hardware which is useful in optimizing and troubleshooting ex
213. ructions in the Getting Started chapter but most of the steps for turning off the spectrometer are already included in this chapter 1 Follow the steps in Section 3 4 except for Step 9 2 Switch the bridge to standby mode Click the standby button Microwave Bridge Tuning es Frequency lt i EES gt wv Stand By Bias Suo am gt Sow v Operate Signal Phase mo Standby SS er hs Auto Tuning Sa DEN Button Te ne uae rea cal v Deva Stop Reference Am Ti von off Dual Trace j7 Attenuation dB E E200 f Log Scale _ a Exel me al Manton Cose Figure 3 27 The microwave bridge tuning dialog box E 580 User s Manual 3 23 Turning the Spectrometer Off 3 Turn off the TWT Press the power switch Power heee e Power Standby Indicator Figure 3 28 The power switch for the TWT 4 Follow the instructions in Section 3 1 of the Bruker E 500 User s Manual Consult the E 500 User s Manual for instructions on disconnecting from the spectrometer powering down the console turning off the magnet power supply and water and logging out of the workstation 3 24 W J A m a One Pulse Experiments 4 For lack of a better criterion to categorize the experiments I have classified them by the number of pulses in the experiment Here we start with one pulse experiments There is only one pulse experim
214. s eSPEL button and the PulseSPEL window appears See Figure 7 3 Load the PulseSPEL variable definitions Click the Load Var Def button and a dialog box will appear ask ing for the file and directory You need to navigate to sharedPulseSPEL Standard PulseSPEL2000 SPEL2 Select the file descr def and click the Load but ton PulseSPEL Programming Panel lt No Name gt dir Load Var Def Button Compile on Button Help On Selection File Edit Search Compile Properties Options He agPgdefload siz Contents of this ae jt PulseSPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File sar def show Filenames Load Cancel Help Load Button Figure 7 4 The PulseSPEL window E 580 User s Manual The HYSCORE Setup Experiment 5 Compile the variable definitions Click the Compile button See Figure 7 4 This compilation initializes all the various delays lengths and counters to the default values 6 Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file hyscore_set exp and click the Load button agPgload Group Contents of this Group PulseSPEL Program Path aredPulseSPEL Standard Pulse SPEL2000 SPEL2 Create
215. s acquired in a conventional field swept experiment Frequency Field Sweep Figure 2 32 Field sweep and frequency spectrum of an E center in quartz are mirror images of each other In Figure 2 33 we see the Larmor frequencies when the field is set so the center line is on resonance The higher field line actu ally has a lower negative Larmor frequency than the center line We need to apply more magnetic field to increase its Lar mor frequency so that it would be on resonance with the micro waves The lower field line has a higher Larmor frequency Aw o o Aw Figure 2 33 Larmor frequencies when B is set for reso nance on the center line E 580 User s Manual 2 33 Pulse EPR Theory Multiple Pulses Echoes 2 1 5 How Echoes Occur As we have seen in the previous sections one microwave pulse produces a signal that decays away FID If our EPR spectrum is inhomogeneously broadened we can recover this disappeared signal with another microwave pulse to produce a Hahn echo Echo DN T st T FID Figure 2 34 A Hahn echo Echoes are important in EPR because FIDs of very broad spectra decay away very quickly We shall see in the second part of this chapter that we cannot detect signals during an approximately 80 ns period after the microwave pulse This period of time is called the deadtime If the FID is very short it will disappear before the deadtime en
216. s equals Number of Scans x Shots per Point C 1 If we wanted to average nine times we have two choices First we could set Shots per Point to 9 and Number of Scans to 1 We would then only see the result at the end of the complete experiment Second we could choose Shots per Point equal to 3 and Number of Scans equal to 3 We still average nine times however the display is updated twice during the experiment with intermediate results It can be useful to monitor intermediate results particularly if you have unstable samples The display of intermediate results does require a small amount of time so the first choice for nine scans would run somewhat faster The number of scans that have been acquired The number of scans that have been averaged This number dif fers from Scans Done if Replace mode is selected E 580 User s Manual The Options Panel The Options Panel C 6 PULSE PATTERNS Figure C 11 The Options panel Acquisition Trigger C 6 1 External Trigger There is an External Trigger input on the PatternJet so that you can trigger an acquisition from an external event such as a laser flash If activated green the External Trigger is enabled The input accepts TTL level signals C 14 BRORER The Options Panel External Trigger Slope Trigger Time Out SRT vs External Trigger Rate External Trigger TRG MON PCLK O Figure C 12 The PatternJet external t
217. s for limiting the detection bandwidth in the video amplifier By using a nar rower bandwidth the high frequency signals that could cause problems are filtered out before they can be digitized 2 56 i Pulse EPR Practice At ns AV R A ZYN _ ki VN MHz 8 J 62 5 1 2y 16 r J 31 25 m 2v 24 J 20 83 te 2v 32 N 1 15 625 Figure 2 58 Fold over effects from not digitizing with sufficient resolution Quadrature signals are shown in the left hand column E 580 User s Manual 2 57 Pulse EPR Practice Dynamic Range In the digitization process the signal is converted into a stream of integers How well this data represents our signal depends on the amplitude resolution of the conversion The SpecJet has a dynamic range of 0 5 Volts and separates this range into 256 8 bits equally spaced steps The digitizer determines which of these 256 steps best matches the voltage of the signal If we wish to distinguish between two signals that are very close in voltage the voltage difference must be larger than the separation of adja cent steps of our digitizer If we do not supply a large enough signal we obtain noisy data exhibiting jagged step like or digiti zation noise See Figure 2 59 It is important to use a video amplifier gain that is sufficient to supply approximately a 0 5 Volt signal to use the digitizer fully S
218. sarily have to understand these equations in Pairs great detail Any functions related by Equation 2 19 and Equa tion 2 20 form what is called a Fourier transform pair The pairs that we shall encounter frequently are shown in Figure 2 21 The important points to learn are V Though a function may be purely real it will in general have Q a complex Fourier transform Even functions f t f t also called symmetric have a The real part of the purely real Fourier transform See Figure 2 21 a frequency domain signal corresponds to e Odd functions f t f t also called anti symmetric have a the absorption and purely imaginary Fourier transform See Figure 2 21 b the imaginary part corresponds to the e An exponential decay in the time domain is a lorentzian in dispersion signal the frequency domain See Figure 2 21 c e A gaussian decay in the time domain is a gaussian in the fre quency domain See Figure 2 21 d 2 24 ekGaen Pulse EPR Theory Notice the similarity of the function in Figure 2 21 e with that in Figure 2 12 Quickly decaying signals in the time domain are broad in the frequency domain Slowly decaying signals in the time domain are narrow in the frequency domain These pairs are reciprocal i e a lorentzian in the time domain results in a decaying exponential in the frequency domain f t F o Re Im a Alt oe ee
219. savwcedusianesed shared 5 1 5 1 Inversion Recovery with FID Detection sesssssessssseessesesssresseserssressesse 5 2 5 2 Standing PA aE CIN a eta d ss rnini a pnd da eae pad es 5 9 5 3 Echo Detected Field Swept EPR 2 40 accatnyo uae cia Mantaneon 5 15 54 T2 Meas rements poseia xadausdocdueneetaugdontwcdtaante a a 5 21 VIII BRUKER Table of Contents 5 5 Field Sweeps with PulseSPE Lia ss cciceshasiechosd cases dea scassaeleaaalardnasiae ceieass 5 25 5 5 1 The Two Pulse Echo Setup Experiment cccccecccssecsseestecsteeeteeeteeneeeens 5 26 5 5 2 The Echo Detected Field Sweep ccccccccsccscessecesceeeeeeeeeseeeeeeneenteeneeeans 5 32 5 6 TWO P lse ESEEM miseire a e aiaa aaa ae nE EAA a ais 5 35 5 7 Advice for Real Samples syeceratevascncvesad ubalsies season destsienn dhedoe neaateovetatadanees 5 45 6 Three Pulse Experiments cccccesessseeeeeeceeeseeeeeeseeseeees 6 1 6 1 Inversion Recovery with Echo Detection ccccecceeescesseceteeeeeeeeeeeeeees 6 2 6 1 1 The Inversion Recovery Setup Experiment c ccccecccesseetsesteeeteeeteentnees 6 3 6 1 2 The Inversion Recovery Experiment 0 cccccsceesecetecetteeteceeeeeeeeeeeeeeeeees 6 10 6 2 Three Pulse ESEEM oralnie irnia e e i a i 6 20 6 2 1 Set p Expertment occa cverdeosrciesteeesetsteesndvan e E EEE E Ei 6 21 6 2 2 Stimulated Echo Decay cccccccccesscescesseesseesecssecneceeeeseeecaeeeseeneeneeneeeses 6 29 DAYS CORES aaee E E A E A
220. se cycle Click the tri angle on the right side and a drop down menu appears display ing the different phase cycles defined in the loaded PulseSPEL program Choose the phase cycle you wish to perform by click ing its name in the list This box is used to edit and display PulseSPEL variables Type the variable name in the PulseSPEL Variable box and then press the Enter key The present value for that variable will appear To change a variable value type variable name lt Space gt followed by the desired value into the PulseSPEL Variable box and then press the Enter key If you wish to verify that the variable value has indeed changed type in the variable name and press the Enter key to view the new value There are four options that can be selected in this drop down menu Normal specifies that the phase cycling proceeds as spec ified in the PulseSPEL program when you click the Run button The next two options are useful for troubleshooting phase cycles Continuous specifies that the presently active step of the phase cycle is repeated continuously e the spectrometer does not proceed to the next step of the phase cycle and repeats the experiment until you press the Run button again Next Cycle advances the spectrometer to the next step of the phase cycle and returns to Continuous mode Skip Program returns the phase cycle to its first step D 22 i Setting up a PulseSPEL Experiment Setting up a PulseSPEL Experiment
221. se separation 2nd pulse initial pulse separation increment pulse separation 3rd pulse initial acquisition delay increment acquisition delay reset separation 2nd amp 3rd pulse Figure 6 28 Original PulseSPEL programs for a 2D stimulated echo experiment 6 30 Three Pulse ESEEM 2D s Ne Ne Ne Ne Ne begin dims end de r begin phi ph2 asgl bsgl end li r r begin r for y swe sh timulated echo use program 2Dstd_set to evaluate timing and amplitude phase settings defs 256 128 Fs lists x X X X x TX X X a a a ta b b b b sts exp SPT QUAD to sy ep x 1 to sx ot i l toh pO ph1 dl dy pO ph2 d2 dx Bt x ne dx nex dx dy next r end ex do dy acq sgl xt i dx d30 t xX 0 dy d31 y P xperiment L Ne Ne Ne Ne Ne Ne e dimension of 2D data array sx sy phase and sign program single point detection lst pulse initial pulse separation increment pulse separation 2nd pulse initial pulse separation increment pulse separation 3rd pulse initial acquisition delay increment acquisition delay reset separation 2nd amp 3rd pulse Figure 6 29 Modified PulseSPEL programs for a 2D stimulated echo experiment E 580 User s Manual 6 31 Three Pulse ESEEM po po N NIA 5 d1 e dy d2 dx d1 do Validate the edited Pu
222. seesseeeteeteeetteensees A 17 A 4 Changing Resonator Modules cccceeccessceesseeeteceseeeeeceeseeceteeneeesaes A 18 A 4 1 Removing a Resonator Module cccceccccsecseceseeseceseeeeeeseeeeeeeeneeeeeeaees A 18 A 4 2 Installing a Resonator Module ccececseesseesceescecseceteceeeeseeeeeeeeseeeseeeeees A 21 A 5 Sample Supports for Split ring Resomators ccceeeeseeseeeteeeeeeeeees A 24 A 0 Microwave Datani cenen ciies decal loante a a tiene a etua hte a ce A 25 Appendix B Integration ccccccssescceeeeseeesseeeeseaeeeeesesenees B 1 B 1 Timebase and Bandwidth cece ccccccssecsteceseceseeeeacecaeceeeseeeeeseeeaeenes B 2 B 2 Shot Repetition Times amp Number of Points ccceeceeseesceeeteeeeeees B 4 Appendix C Overview of Parameter Panels 00068 C 1 C 1 Common Buttons and Commands cecceesceceseceeeceeeeeeeeenseceteeeeeeenees C 1 C2 The Patterms Panel lt 3 scavevancnsAnieles dats wae aia daa iis aes C 2 Ci2 Edit Commands e a eraa ea oE AET rr Ea ERE ATA REEE C 4 G 2 2 Number of Pommits cscs unnan eiretie ieii n ie EEE EEEE a C 7 C 3 The Field ane sats sizes econ tic zest sess ea ae ask Su datas ules tats cs Ot Senshi C 8 Ca The Acquisition Panelini tee ste ansihy esa EES wanes C 10 C 4 1 Abscissa Quantities and SiZes ccccecccccssscesssecessccesseeessceeessecesseceseeenses C 10 C42 Acquisition Mode pieren i aie e a eE iare C 11 C 4 3 PulseSPEL Acg isition se nnie n
223. ser s Manual B 3 Shot Repetition Times amp Number of Points Shot Repetition Times amp Number of Points B 2 Short shot repetition times SRT restrict the number of points that can be integrated or conversely more acquired and inte grated points results in a slower acquisition In order to most efficiently acquire spectra for a given number of integration points the SRT must be greater than or equal to values shown in Figure B 2 Of course a long T may demand an even longer SRT If you are using a PulseSPEL program the number of integrated points is equal to pg integrator time base If you are using the pulse tables the number of points is equal to the acqui sition trigger length integrator time base SpecJet PatternJet in QUAD MODE minimum SRT psec 64 128 256 512 1024 2048 number of Integration points Figure B 2 Minimum shot repetition time vs number of integrated points Overview of Parameter Panels C The six panels of the FTEPR Parameters window give you access to the parameters required for a pulse experiment This appendix defines and describes the many parameters you will need to perform your pulse experiments The appendix con cludes with a description of the SpecJet display Common Buttons and Commands C 1 Close PulseSPEL Help Up Arrow Down Arrow lt Ctrl gt Arrow lt Shift gt Arrow The following three buttons are in each of the six parameter p
224. signal decreases the oscil lations in the FID become slower E Figure 2 30 The effect of line splittings E 580 User s Manual 2 31 Pulse EPR Theory lt If we are not exactly on resonance with the center of a sym metric signal we will get an oscilla tion between the real and imaginary com ponents U 7 HE Lu Ni E i AQ Figure 2 31 The effect of a frequency shift These practical examples demonstrate that if we make use of the Fourier transform pairs properties and convolution theorem we can easily envision how signals appear in both time and fre quency domains We do not have to perform any complicated mathematical operations to Fourier transform our signals We can visually estimate the appearance of signals in both the time and frequency domains Even though this intuitive ability is not mandatory it comes in very handy later on when we shall be adjusting parameters and processing data 2 32 Pulse EPR Theory Field Sweeps vs Frequency Spectra 2 1 4 A little bit of care is required when comparing conventional field swept spectra and frequency spectra obtained by FT EPR The field and frequency axes run in opposite directions Here are two spectra of the same sample The upper spectrum is a frequency spectrum acquired by Fourier transforming the echo To be dis cussed in the next section The lower spectrum wa
225. sk clock wise to tighten the sample holder See Figure A 7 Reinsert the sample and check for fit f fe ae ON Adjustment dA se Figure A 7 The end of the sample holder Resonator Description Correct length adjustment is very important for the successful operation of the resonator The sample center not the bottom of the sample should extend approximately 39 mm from the end of the sample holder When the sample holder and sample rod are fully inserted in the FlexLine resonator the sample will be positioned properly in the resonator M 39 mm Figure A 8 Centering the sample in the resonator The Pulse ENDOR resonator is slightly different it requires a distance of approximately 55 mm in order to properly center the sample Sample tubes for the Pulse ENDOR reso nator must be less than 4 mm in diame ter and have a round bottom E 580 User s Manual A 9 Resonator Description The Sample Rod A 1 4 The sample rod is used to insert and remove samples The sam ple holders described in the previous section screw into the end of the sample rod See Figure A 9 On top of the sample rod is a stopper for ventilation If you are performing cryogenic exper iments it allows you to vent the sample rod of air There is an o ring which makes the seal It is good practice to periodically examine the o ring to ensure that it is still in good condition To insert the sample into
226. ss can often be obtained resulting in a 7 2 pulse length of approxi mately 9 ns The effect of a 2 2 pulse is shown in Figure 2 6 it results in a stationary magnetization along the y axis If we y J A m a i Pulse EPR Theory were to make the pulse twice as long we would have a n pulse and the magnetization would be rotated to the z axis MW ON MW OFF Figure 2 6 The effect of a 7 2 pulse Because B is parallel to x it is known as a x pulse If we were to shift the phase of the microwaves by 90 degrees B4 would then lie along the y axis and the magnetization would end up along the x axis Microwave pulses are therefore labeled not only by their tip angle but also by the axis to which B is paral lel Figure 2 7 Four different pulse phases E 580 User s Manual 2 9 Pulse EPR Theory Viewing the In the introduction it was mentioned that the sample emitted Magnetization microwaves after the intense microwave pulse How this hap from Both T pens is not completely clear if viewed from the rotating frame If S viewed from the lab frame the picture is much clearer The sta tionary magnetization along y then becomes a magnetization rotating in the x y plane at the Larmor frequency This generates currents and voltages in the resonator just like a generator See v Figure 2 8 and Figure 2 9 The signal will be maximized for the magnetization exactly in the x y plane
227. sweeps ns i e pulse separation where TWT gate pulse can be split i end defs PulseSPEL is not case sensitive therefore we do not need to worry whether a particular letter is upper or lower case Com ments text not to be interpreted by the compiler are preceded by a semicolon All PulseSPEL variables are integers The default unit for pulse lengths and delays is ns nanoseconds You can specify other time units such as us microseconds ms milliseconds or s seconds For example d0 10 us DEFS Section PulseSPEL needs to know where the variable definitions start and stop The start is indicated by begin defs and the end by end defs General Variables There are 26 single character variable names Two X and Y are reserved for use as indices or loop counters for the x and y axes E 580 User s Manual D 3 The PulseSPEL Programming Language Delay Variables Increment Variables Pulse Length Variables Spectrum Size Variables RF Variables There are 32 delay variables DO D31 These variables deter mine the time between events There are two delay variables DX and DY that determine the step size or resolution of the x and y axes There are 32 pulse length variables PO P31 These variables determine the lengths of pulses Two spectrum size variables SX and SY are the number of points along the x and y axes respectively They are implicitly defined by the dimension statement i
228. th Order Slice current Val Oth Order 106 Ist Order Left 0 1st Order Right 0 Add 2Pi 0 zi Phase angles specified in degrees Use Position Qualifier to indicate Left amp Right positions Apply Close Button Button Figure 4 31 The Phase dialog box o GHz 0 099999 Figure 4 32 Properly phased data from Section 4 1 3 Please decide Move result to input Button 0 049999 0 099999 E 580 User s Manual 4 25 Processing the FID 0 049999 0 099999 04 0 05 o 0 049999 0 099999 Figure 4 33 Properly phased data from Section 4 2 Magnitude Spectra 4 3 5 There is still one more option if we have spectra that are not phased properly We can eliminate the phase information by cal culating a magnitude spectrum with the following formula magnitude Vcomplex x complex 4 1 where signifies the complex conjugate The phase factor we saw in Equation 2 22 cancels out because iot Hot e e 1 4 2 This approach has one drawback namely it produces spectra which are broader than absorption spectra This can be seen in Figure 4 34 the imaginary part is broader than the real part and hence contributes to the broadening of the magnitude spectrum 4 26 W J A m a i Processing the FID Magnitude Real Imaginary d1 0 05 o 0 049999 0 099999 GHz Figur
229. the phase cycle 13 Save the spectrum 6 28 shg Three Pulse ESEEM 14 Find where the top of the echo bottom is Place your cursor on the spectrum and determine from the read out at what time the top of the stimulated echo occurs See Figure 6 27 Record this number somewhere We shall use this value for dO in the next section Figure 6 27 The stimulated echo after a four step phase cycle Stimulated Echo Decay 6 2 2 1 Follow the instructions of Section 6 1 1 2 Edit the PulseSPEL program The standard Puls eSPEL program needs a bit of modification to suit our needs so this is an excellent opportunity to learn how to modify pulse programs Make the changes indicated in Figure 6 29 Only one line needs to be added E 580 User s Manual 6 29 Three Pulse ESEEM 2D stimulated echo i i and amplitude phase settings i begin defs dim s 256 128 end defs r begin lists phl x x x X ph2 x x xX xX asgl a a a a bsgl b b p Fb end lists r r begin exp SPT QUAD for y 1 to sy sweep x 1 to sx shot i 1 to h pO ph1 d1 dy pO ph2 d2 ax po x do dy acq sgl next i dx dx d30 next x dx 0 dy dyt d31 next y end exp xperiment use program 2Dstd_set to evaluate timing Ne Ne Ne Ne Ne Ne Ne Ne Ne dimension of 2D data array sx sy phase and sign program single point detection lst pulse initial pulse separation increment pul
230. these two operations in reverse order may lead to damage to the CW detector Set the HPP attenuator to 60 dB HPP Attenuator T BRUKER PULSE BRIDGRYONTROLLER 0 CO cw LPP Lew WAKEUP 5V Sy ae dB o o 0 9 0 Q aolo IND ALT DIG o o o i READY 5V 145V 20V Figure 3 25 Buttons on the pulse bridge controller 3 Power Switch Switch the TWT to standby mode Press the standby button on the TWT o o Standby Button N Power Figure 3 26 The standby button for the TWT 4 Press the AMP button The LED will go out when it is deactivated This turns off the preamplifier Press the HPP button The LED will go out when it is deactivated This turns off the pulse excitation mode Press the QUAD button The LED will go out when it is deactivated This switches the detection from the quadrature detector to the CW detector Press the CW button The LED will light when it is activated This turns on the CW excitation mode E 580 User s Manual 3 21 Changing Samples Remove the sample Refer to Appendix A for details on changing samples Follow the instructions of Section 3 2 and Section 3 3 3 22 C gt BROKER LS Turning the Spectrometer Off Turning the Spectrometer Off 3 5 It may seem a bit unusual to have shutting down inst
231. this number somewhere We shall use this value for dO in the next section Bottom of Echo Figure 7 10 The inverted echo E 580 User s Manual The HYSCORE Experiment The HYSCORE Experiment 7 2 1 Follow the instructions of Section 7 1 2 Launch the PulseSPEL window Click the Puls eSPEL button and the PulseSPEL window appears See Figure 7 3 3 Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file hyscore exp and click the Load button agPgload Group Contents of this Group Icw_detection peanut 4 Pulse SPEL Program Path aredPulseSPEL Standard PulseSPELZ000 SPEL2 Create Fle hyscore exp show Filenames 7 Load Cancel Help Load Button Figure 7 11 Selecting the PulseSPEL program 4 Edit the PulseSPEL program The standard Puls eSPEL program needs a bit of modification to suit our needs Make the change indicated in Figure 7 12 The HYSCORE Experiment begin defs dim s 150 150 end defs r begin lists phl x x xX X ph2 x x x xX asgl a a ta a bsgl b b b b end lists L r begin exp SPT QUAD r dx 0 dy 0 for y 1 to sy sweep x 1 to sx shot i 1 to h po x po x p2 ph1 pO ph2 acq sgl next i dx dx d30 next x dx 0 dy dy
232. through 8 for the imaginary trace We need to baseline correct the imaginary compo nent as well as the real Exit the polynomial baseline correction task bar Click the Return button in the task bar Remove the Qualifier Click the a button in the tool bar E 580 User s Manual 4 17 Processing the FID Left Right Shift 4 3 2 In Section 4 1 1 we acquired not only the FID but also the microwave pulse leak through and the deadtime This part of the trace does not contain any useful information for us Experimen tal means of removing this extraneous information was pre sented in Section 4 1 2 and in Step 10 and Step 11 of Section 4 2 Here we shall learn how to remove this extraneous information with the software if we have not removed the dead time data by changing the delay 1 Select the Left Right Shift command Click its but ton in the Transformations submenu of the Processing menu Processing Diff amp Integ F Transformation mtenng id Algebra Submenu Peak Analysis Complex Window Functions Transformations F bnagiig Zero Filling pie _ FFT Structure FFT Real XSophe 2D FFT ProDeL Cross Term Averaging Automatic z Convolitien undo Deesavanition 42 Symmetrization Invert Abscissa g Factor Left Right Shift Normalize Axes Normalize Spectrum Command Normalize Integrals Phase
233. to C 15 adjusting 4 6 5 4 5 16 5 22 aliasing 2 56 to 2 57 AMP button 3 21 B B 2 6 to 2 14 2 44 bandwidth detection 2 47 2 53 excitation 2 52 to 2 53 baseline correction FID 4 14 to 4 17 HYSCORE 7 14 to 7 16 three pulse ESEEM 6 34 to 6 36 Bee 2 13 bibliography 2 67 to 2 73 EPR 2 68 to 2 71 NMR 2 67 to 2 68 Pulsed ENDOR 2 71 to 2 73 Boltzmann distribution 2 5 2 15 button AMP 3 8 center C 9 CW 3 3 3 8 3 21 HPP 3 8 3 21 left C 8 QUAD 3 8 3 21 right C 9 run 3 14 C 19 STAB 3 3 start 3 15 C 3 stop 3 20 C 19 C center field C 8 changing samples E 580 User s Manual Index low temperature A 15 to A 16 room temperature 3 20 to 3 22 channel a amp b 2 46 selection C 3 convolution theorem See Fourier theory convolution theorem coupling adjustment 3 6 A 4 A 5 D data acquisition 2 50 to 2 60 integrator 2 52 to 2 54 point digitizer 2 51 transient recorder 2 55 deadtime 2 34 2 44 to 2 45 2 61 finding end 4 12 defense diode 2 44 pulse 3 17 detection 2 44 to 2 47 Also see data acquisition non selective 2 52 selective 2 52 dip external stabilizer 3 5 to 3 6 resonator 3 5 to 3 6 dynamic range 2 58 to 2 59 E editing table values C 4 to C 6 cleanup channel C 6 clear column C 6 copy channel C 5 cut channel C 5 delete column C 6 deselect all C 5 insert column C 6 paste channel C 5 repeat group C 6 select all C 5 effective magnetic
234. to phase the data to obtain pure absorption and dis persion spectra These procedures are described in this section Baseline Correction 4 3 1 For FIDs that are acquired with the pulse tables i e no phase cycling we need to subtract any DC offsets This procedure is not required for the data set we acquired with the PulseSPEL program because the phase cycle cancels the offset effects 1 Create a new viewport The data we have is complex having both real and imaginary parts so it is advanta geous to view both parts simultaneously with two linked viewports Click split hor or split ver in the New 1D Viewport submenu of the Viewports menu I have chosen vertical to fit the images better on the page Viewports Current Viewport Gear current New 1D Viewport F New 2D Viewport Split hor 1D lt gt 2D Remove Viewport Link Viewports Unlink Viewport Figure 4 15 Creating a new viewport i Processing the FID 2 Switch the new viewport to display the imaginary component Select the new viewport by clicking its selection bar Click the Re Im button to toggle the display from real to imaginary The dataset display indicates the status by a Re or Im suffix for real and imaginary parts respectively Yj Dp Pe zj Z 2 v gt 5 ae al A A aj aj al mj f ej oj uj a FS v A e ES w feno Secon
235. ton Compile Button Figure 6 3 Launch the PulseSPEL window Click the Puls eSPEL button and the PulseSPEL window appears See Figure 6 3 Load the PulseSPEL variable definitions Click the Load Var Def button and a dialog box will appear ask ing for the file and directory You need to navigate to sharedPulseSPEL Standard PulseSPEL2000 SPEL2 Select the file descr def and click the Load but ton PulseSPEL Programming Panel lt No Name gt dir Help On Selection File Edit Search Compile Properties Options He agPgdefload Ci F Pulse SPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File sar def 1 show Filenames Load Cancel Help i a A of this Group Load Button The PulseSPEL window Inversion Recovery with Echo Detection The PulseSPEL edi tor works very much like any standard text editor For details see Appendix D Compile the variable definitions Click the Compile button See Figure 6 3 This compilation initializes all the various delays lengths and counters to the default values Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file echo_ir exp and click the Load button
236. trolled by selecting either Next or Previous Selecting All will find all incidences of the Search String in the current document The Scope of the search can be restricted to only the selected text in the current document or above and below the present cursor position Click Search and the cursor will move to the first incidence of the Search String in the current document Click Close to close the dialog box agPgFind Search String Scope Entire Text al Search Selected Text Above Cursor Below Cursor Figure D 21 The Search String dialog box Search Selection Searches for the Search String from the present cursor position Forward to the end of the document D 38 i PulseSpel Programming Panel Search Selection Backward Replace String Compile Compile Searches for the Search String from the present cursor position to the beginning of the document This command operates in a similar fashion to the Search String command Enter the replacement text in the Replace String box When you click Replace the next incidence of the Search String in the document is replaced by the Replace String If the All options is selected all incidences of the Search String are replaced with the Replace String agPgReplace Search sting Replace String Saas rete scope enrere v Replace dose Help Figure D 22 The Replace String dialog box D 4 4 This drop
237. up to and including Section 3 3 using the coal sample as your sample 2 Click the Stop button The PatternJet pulse program mer stops See Figure 5 10 E 580 User s Manual 5 9 A Standing Hahn Echo 3 Program two 16 ns x pulses 400 ns apart FT EPR Parameters Pattems l Field RF Acquisition Scan Options PULSE PATTERNS Channel Selection x al Shot Rep Time us 999 60 Shots Per Point 1 z Edit Position ns Length ns 16 fe foe r Pos Disp ns a Start amp Stop Tenth tece a lo a Buttons ee Cose PulseSPEL Help Figure 5 10 Programming two 16 ns x pulse 400 ns apart 4 Program a 20 ns Acquisition Trigger pulse start ing at 0 ns Click the Start button The PatternJet pulse program mer starts again See Figure 5 10 Open the SpecJet window If the SpecJet window is not open click its button Select for Repetitive Mode Press the Run button See Steps 8 through Step 11 of Section 3 3 A Standing Hahn Echo 7 Set the HPP attenuator to about 5 dB See Figure 3 10 8 Adjust the Center Field to about 3430 G and the Sweep Width to 100 G 10 000 5 000 hmar AM EN EOE o himen em i a ean ren 5 000 10 000 0 500 1000 1500 2 000 i Timefns Figure 5 11 An off resonance coal echo 9 Adjust the VAMP gain Decrease or increase the gain
238. ur steps of the phase cycle as well as jump far off resonance and subtract this background Run Button Figure 4 12 The Run button 10 Find where the deadtime ends Place your cursor on the spectrum and determine from the readout at what time the deadtime ends See Figure 4 13 Record this num ber somewhere In this case it happens to be 480 ns but the value is spectrometer dependent idet FS Y idet ES YF lt no Secondary gt __ S sno Resuit gt Y sno quaiinier gt 30 000 30 000 20 000 r 20 000 121 480 14337 10 000 10 000 0 10 000 10 000 20 000 20 000 a SSS SS SS SSS SS SSS SSS s Ilo 500 1 000 1 500 2o90 S Jo 500 1 000 1500 2 000 Intensity xX 480ns y 1 434e 04 Time ns Intensity J Time ns Figure 4 13 Finding the end of the deadtime and the beginning of the FID Acquiring a FID with PulseSPEL 11 Set d0 to the proper value dO is the delay for the Acquisition Trigger so that it starts to digitize at the desired initial time First we need to find the default value Type dO in the PulseSPEL Variable box and then press the Enter key The present value for dO will appear The new value we need to enter is equal to the sum of this value of dO plus the delay we determined in Step 10 In this example it equals 40 480 520 ns Type dO lt Space gt followed by the value you have calculated
239. ure 5 30 4 Load the PulseSPEL variable definitions Click the Load Var Def button and a dialog box will appear ask ing for the file and directory You need to navigate to sharedPulseSPEL Standard PulseSPEL2000 SPEL2 Select the file descr def and click the Load but ton PulseSPEL Programming Panel lt No Name gt dir File Edit Search Compile Properties Options He Load Var Def Button agPgdefload siz 2 a A of this pa g Pulse SPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File sar def show Filenames Load Cancel Help Compile Dem Button Load Button Help On Selection Figure 5 30 The PulseSPEL window E 580 User s Manual 5 27 Field Sweeps with PulseSPEL 5 Compile the variable definitions Click the Compile button See Figure 5 30 This compilation initializes all the various delays lengths and counters to the default values 6 Load the PulseSPEL program Click the Load Pro gram button and a dialog box will appear asking for the file and directory You need to navigate to sharedPuls eSPEL Standard PulseSPEL2000 SPEL2 Select the file echo2phi exp and click the Load button agPgload Group Contents of this Group PulseSPEL Program Path aredPulseSPEL Standard PulseSPEL2000 SPEL2 Create File echo2phi exp show Filenames Pa
240. ute to the echo decay In all we have said so far we should be able to make t the pulse separation very long and still obtain an echo Transverse relax ation leads to an exponential decay in echo height Echo Height t ce 2 28 where Ty the phase memory time is the decay constant Many processes contribute to Ty such as T spin spin relaxation as well as spectral spin and instantaneous diffusion Notice the factor of two in Equation 2 28 which is not in the expression for the FID This is because dephasing starts after the first pulse and the echo occurs at 21 after the first pulse So by studying the echo decay as we increase t we can measure Ty Spectral diffusion often is a large contributor to Ty Nuclear spin flip flops molecular motion and molecular rotation can cause spin packets to suddenly change their frequency A faster spin packet far from the y axis will suddenly become a slower spin packet without the needed speed to catch up with the other spin packets in their race to refocus Therefore we are not refo cusing all the magnetization In Figure 2 37 we see that after the runner marked with an asterisk has a shifted frequency we only get four of the five runners lining up to refocus n Pulse Figure 2 37 Dephasing due to a sudden frequency shift The asterisk marks the runner whose frequency has suddenly become less 2 36 Pulse EPR Theory ESEEM A very important class of echo
241. values in the table can be saved on the hard disk as well as loaded back into the table The files are stored in the directory usr xepr AcquisitionServer OS9 Servers E580 FUSETUP FUFTEpr XBand These configuration files only contain information regarding the pulse operation They are not the same as spectrometer ini Indicates the name of the present pulse configuration file Loads a new pulse configuration file Saves the present values in the current configuration file Deletes the current configuration file from the hard disk E 2 2 The amount of gate time required before the TWT amplifies the microwaves without phase and amplitude distortion The TWT cannot be gated continuously If the TWT gate length exceeds this value the software will stop the experiment and display an error message This is typically 10 000 ns The minimum time between TWT gates The maximum TWT duty cycle If this value is exceeded the software stops the experiment and displays an error message The maximum RF duty cycle for pulsed ENDOR experiments If this value is exceeded the software stops the experiment and displays an error message The duty cycle must yield an average power of less than 20 W This corresponds to 4 and 10 for 500 W and 200 W RF amplifiers respectively C gt BROKER LS Configuration and Timing Pulse Programmer Setup E 2 3 Channel Time Raster PDCH Board Connector Delay Length On the left hand s
242. w have two new Fourier transform pairs f t g t gt F Go 2 25 F G amp f t g t 2 26 So the convolution theorem gives us an easy way to calculate a convolution integral if we know the individual Fourier trans forms More importantly it offers us a powerful means of envi sioning time signals in the frequency domain and vice versa 2 28 W J A m a i Pulse EPR Theory A Practical Now its time to start applying what we have learned in the previ Example ous sections to a concrete problem predicting what a time domain signal e g a FID looks like if we are given a frequency domain signal e g an EPR spectrum As an example we con sider a three line EPR spectrum such as a nitroxide See Figure 2 25 We assume that the magnetic field is set so that the center line is on resonance the lines are lorentzian and the splitting is equal to A Remember that in an FT experiment we are detecting both the absorption real and dispersion imagi nary signals AA g E e eee A 0 A Figure 2 25 A three line EPR spectrum with both absorptive and dispersive components The first thing to notice is that we can deconvolute the spectrum into a stick spectrum and a lorentzian function Pi jt tu AHP Figure 2 26 Deconvoluting a three line EPR spectrum into a stick spectrum and a lorentzian function E 580 User s Manual 2 29 Pulse EPR Theory
243. wo pulse echo acquisition standing 5 9 to 5 14 TWT 2 43 operate mode 3 18 standby mode 3 21 turning off 3 24 turning on 3 2 typographical conventions 1 3 U unwanted echoes amp FIDs 2 66 V VAMP video amplifier 2 47 bandwidth 3 2 gain 3 2 adjusting 5 11 variable temperature operation A 15 to A 16 W water connections A 6 waveguide gasket A 12 window function HYSCORE 7 17 to 7 18 three pulse ESEEM 6 36 to 6 37 two pulse ESEEM 5 40 to 5 41 i
244. x y y asgl ta a b b bsgl b b a ta end lists In the first step of the phase cycle a X microwave pulse is applied and the data from the first quadrature detection channel is added to the real component of the dataset and the data from the second quadrature detection channel is added to the imagi nary component of the dataset The second step of the phase cycle differs from the first in that a X microwave pulse is applied and the data are subtracted from the real and imaginary channels of the dataset The third step is slightly more complicated because we are swapping the quadrature detection data A Y microwave pulse is applied Data from the second quadrature detection channel is added to the real component of the dataset and data from the first quadrature detection channel is subtracted from the imaginary component of the dataset It is left as an exercise to determine what happens in the fourth step of the phase cycle Each of the definitions in the lists section do not have to be the same length For example begin lists pho x phil x x x x asgl ta a bsgl b b end lists is a valid phase cycle The shorter definitions are repeated until they are the same length as the longest definition Therefore our example is equivalent to D 6 The PulseSPEL Programming Language Experiment Section begin lists PRO x x x X phl x x x X asgl a a bsgl b end lists a
245. y achieve a B of 10 Gauss in the rotating frame If we have features narrower than 10 G in an analogous fashion to field overmodulation the power broadening will decrease our resolution In CW EPR we turn down the field modulation In pulse EPR we can use softer pulses to achieve the need for better resolution See Figure 2 54 16 ns Figure 2 54 Linewidths for different pulse lengths with non selective detection for echo detected field swept spectra 2 52 Pulse EPR Practice What we have essentially done is limit the bandwidth of excita tion By using an integrator we can also limit the bandwidth of detection It is the off resonance high frequencies that contribute to the power broadening If we are able to filter the high fre quency components out we can regain our resolution even with hard pulses By integrating the area under the echo we can achieve this filtering How this filtering is accomplished can be seen in Figure 2 55 On resonance the area under the echo is large and positive If we go off resonance we obtain the high frequency components with negative going contributions These negative signals cancel out the positive signals when we inte grate the echo effectively achieving the desired filtering effect The longer period of integration time the more effective and selective the bandwidth limitation becomes See Figure 2 56 and notice the similarity with Figure 2 54 On Resonance Integrated Area
246. y all the compilation messages If not active the only messages displayed are either error messages or messages stating that the compila tion or validation has been successful The display area will show the variable definitions instead of the PulseSPEL program D 4 5 This drop down menu contains commands associated with the appearance of the PulseSPEL Programming Panel Figure D 24 The Properties menu D 40 W J A m a i PulseSpel Programming Panel Show Buttons Panel Position Options Buttons Displays or hides the buttons on the left hand side of the panel See Figure D 9 Click this command and a dialog box appears displaying the coordinates and dimensions of the PulseSPEL Programming Panel The values can be edited and the new values are set by clicking Apply Close closes the dialog box agPgPanel x fos a width z4 Height 750 Select server and click OK HEHEHEHE Figure D 25 The Panel Position dialog box D 4 6 This drop down menu contains commands associated with panel properties Consult the Xepr User s Manual for details on panel properties Figure D 26 The Options menu D 4 7 The most commonly used commands can be accessed through the buttons on the left hand side of the panel E 580 User s Manual D 41 Pulse Tables vs PulseSPEL Pulse Tables vs PulseSPEL D 5 In Chapter 5 we measured T with the pulse tables
247. you do you run the risk of damaging the pulse bridge E 580 User s Manual 3 17 Safety Test 15 Switch the TWT to operate mode Press the operate button on the TWT In about 15 seconds the TWT will be in operate mode Power Operate Button Switch N Power Standby Figure 3 21 The operate button for the TWT Indicator 16 Slowly decrease the HPP attenuator Look for evi dence of ring down This is microwave power from the pulse that has not fully dissipated after the defense pulse Do not confuse it with the microwave pulse which occurs If you still see A A ring down despite during the defense pulse Usually excessive Q causes the increasing the cou ring down after the defense pulse If you see ring down pling stop decreas stop decreasing the HPP attenuator and increase the cou ing the attenuation pling See Figure 3 6 and heed the warning next to the and call your local Bruker EPR repre sentative for assis tance figure until the ring down disappears If you do not see evidence of excessive ring down continue until you have reached about 4 5 dB Your SpecJet trace should qualita tively resemble the right trace in Figure 3 22 Sometimes you may be in resonance with an EPR signal and you can see a FID that can be confused with ring down See Figure 3 23 You can verify that it is a FID by changing the magnetic field If the signal changes it is a FID and not ring down

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